The German's Finnish teammate Kimi Raikkonen sealed the Ferrari front-row lockout.
Hamilton, who clinched his fourth world championship in Mexico two weeks ago, started from the pitlane after crashing in qualifying but led the race after 31 of 71 laps when others pitted.
The German, whose last victory was in Belgium in August 2018, took the chequered flag 2.641 seconds ahead of Monegasque team mate Charles Leclerc, who had started on pole position for the third race in a row.
Sebastian Vettel clocked a best lap in one minute and 40.464 seconds to outpace nearest rival and championship leader Valtteri Bottas of Mercedes by 0.272s.
Sebastian Vettel lost his second-place finish after being disqualified by stewards for a fuel irregularity.
The pole was the Finn's second in a row, after Brazil two weeks ago, and fourth of the campaign. Hamilton had been aiming for his 12th of the year.
Max Verstappen led a soggy Monaco Grand Prix from start to finish on Sunday
The German, a four times world champion, was given a 10 second stop-and-go penalty during the race for angrily banging wheels with his Mercedes rival while they were behind the safety car.
Ferrari's Sebastian Vettel, winner of 52 races, has gone more than a year since he tasted victory at last year's Belgian race.
Carlos Sainz put Ferrari on pole position for the US Formula One Grand Prix in Austin, Texas, on Saturday, with Red Bull's double World champion Max Verstappen joining the Spaniard on the front row.
Quadruple world champion Sebastian Vettel will replace Fernando Alonso at Ferrari next season after signing a three-year deal, the Italian team said on Thursday.
Ferrari's Sebastian Vettel said he would still sleep soundly despite a mistake that cost him a home German Grand Prix win at Hockenheim and the Formula One championship lead on Sunday.
Sebastian Vettel, who joined in 2015 with the dream of emulating boyhood hero Michael Schumacher in winning titles with the sport's oldest and most glamorous team, is out of contract at the end of the year.
Sebastian Vettel was Ferrari's first choice to stay and partner Charles Leclerc in Formula One next year until the COVID-19 pandemic changed everything, team principal Mattia Binotto said on Friday. The four-times World champion, who won his titles with Red Bull, will now be replaced by Spaniard Carlos Sainz who joins from McLaren at the end of the season in a decision announced in May.
Sebastian Vettel believes the back-to-back races in Austria at the start of the Formula One season will be decided on slim margins and his Ferrari team will need to fine-tune their racing strategy to remain competitive over two weeks. Four-times World champion Vettel and team mate Charles Leclerc hit the track in Ferrari's 2018 car, the SF71-H, earlier this week in a test at Mugello as the Scuderia stepped up their preparations for the 2020 campaign.
Sebastian Vettel recognised that he and Ferrari have made mistakes this season but refused to single out the moment where his hopes of winning a fifth Formula One title ended.
Mercedes' seven-times world champion Lewis Hamilton, and now-retired four-times champion Sebastian Vettel, have been among those making political statements at races in recent seasons.
This is the German's 50th career win
Four times Formula One champion Sebastian Vettel recognised he is sailing through a 'rough sea' but said on Thursday there had been no talks with Ferrari about parting ways before the end of the season.
Sebastian Vettel trimmed Lewis Hamilton's Formula One lead to 17 points with eight races remaining.
Ferrari's Formula One world championship leader Sebastian Vettel was handed a five-second penalty for colliding with the Mercedes of Valtteri Bottas on the opening lap of the French Grand Prix on Sunday.
Team-by-team prospects for the Formula One season starting in Melbourne, Australia, on March 17
Formula One leader Lewis Hamilton put Mercedes on pole position for their 200th race at the German Grand Prix on Saturday while engine problems dashed Ferrari's hopes.
Ferrari are not extending Sebastian Vettel's contract beyond this year
Protesters blocked several roads and police fired teargas at a school in Bahrain on Sunday, activists said, as the Gulf state staged a Formula One race promoted by the government as pure sport but seen by the opposition as a public relations stunt.
Lewis Hamilton tightened his grip on securing a fifth Formula One world title by coming from nowhere to claim a stunning pole position for the Singapore Grand Prix in his Mercedes on Saturday.
The Indian Grand Prix saw Sebastian Vettel and Fernando Alonso on the top of their respective games. Raja Sen looks back on Sunday's duel.
"I'm just extremely grateful that I'm here, and tonight I'm going to call my family and all my loved ones. I passed two metres from that crane. If, I had been two metres to the left, I would have been dead."
Charles Leclerc seized the first pole position of his Formula One career on Saturday with Ferrari team mate Sebastian Vettel second fastest to lock out the front row for the Bahrain Grand Prix.
Ferrari boss Mattia Binotto said the pair remain free to fight on track and if either is clearly faster than the other would be given preference.
Ferrari announced a restructuring of their Formula One technical department on Wednesday after struggling in the first three races of a season so far dominated by Mercedes. The sport's oldest, most glamorous and successful team -- last year's runners-up -- are fifth in the championship with Sebastian Vettel and Charles Leclerc pushed into more of a midfield battle.
Ferrari's Sebastian Vettel, the Briton's closest rival, finished only sixth after an early collision with Red Bull's Max Verstappen left the German fighting back from 19th place.
Red Bull Formula One drivers Mark Webber of Australia (left) and Sebastian Vettel of Germany (right) play cricket during a press event before the first day of the Australian F1 Grand Prix on St. Kilda Beach in Melbourne.
Four-time Formula One world champion Sebastian Vettel will race for Aston Martin, the new name for the Canadian-owned Racing Point team, on a multi-year deal after leaving Ferrari at the end of the season.
The Dutch driver won the race at Suzuka, with Leclerc demoted from second to third behind Red Bull's Sergio Perez for cutting the final chicane while defending from the Mexican on the last lap.
Four-time world champion Sebastian Vettel has joined the bandwagon of drivers opposing the newly proposed aggregate qualifying format of the Formula One. According to the latest qualifying format, a driver's two best laps in each of the three knockout sessions will be combined in order to determine the grid position. Meanwhile, the 90-second qualifying format that saw the drivers get eliminated one by one rather than being dismissed at the end of each session in the season-opening Australian Grand Prix and in the Bahrain Grand Prix would be dropped. Hitting back at the new format, the Ferrari driver compared the new system with the circus and insisted that the F1 should focus only on racing, the Guardian reported Echoing similar views, Mercedes executive director Toto Wolff described the new format as `madness` and said that all the teams wanted to revert back to that of the previous season.
Triple Formula One world champion Lewis Hamilton smashed the Bahrain circuit lap record on Saturday to take pole position ahead of Mercedes team mate Nico Rosberg for Sunday's grand prix. The Briton's best lap of one minute 29.493 seconds was the fastest ever at the Sakhir track. Ferrari's Sebastian Vettel and Kimi Raikkonen qualified third and fourth for the second race of the season.
The 2013 Formula One season starts March 17. Check out the team line-ups.
Formula One photographer Mark Sutton had reported seeing the German getting into the passenger seat of Szafnauer's Ferrari after the race at Silverstone, but was unable to take pictures.
Four-times world champion Sebastian Vettel won the Australian Grand Prix for Ferrari on Sunday to dash Mercedes' hopes of extending their dominance into a fourth successive season of Formula One.