Spain's Gorka Izagirre took second place and Yates finished third, 15 seconds behind.
The World No 1 sustained the pace in the climbs up to the Col de Vars and the Col d'Izoard, both culminating at more than 2,000 metres, but then lost ground when his compatriot Thibaut Pinot accelerated to rein in defending champion Geraint Thomas.
'It's a big emotion because I've won on the Tour. I haven't won (a race) since the start of the season. It's great to make it. It was tough but I'm super happy to have won.'
Makes us wonder how these cyclists don't fall short of breath as they pedal to the finish line. Here's a glimpse of the tricky but beautiful terrain that outlines the Tour de France...
Frenchman Alaphilippe retains lead.
The Tour de France has been postponed to August 29-September 20 due to the novel coronavirus pandemic, the International Cycling Union (UCI) said on Wednesday. French president Emmanuel Macron said on Monday that no public event would take place in the country until mid-July as part of measures to contain the coronavirus outbreak, which has infected over two million people worldwide.
Team Ineos's Luke Rowe and Lotto Jumbo-Visma's Tony Martin were both kicked out of the race following an altercation, just under 14 kilometres from the finish.
Briton Adam Yates retained the overall leader's yellow jersey after staying tucked in the main peloton, which crossed the line with a deficit of 2:53.
World champion Peter Sagan claimed his third 2016 Tour de France stage victory when he pipped Alexander Kristoff on the line at the end of the 16th stage, a 209-km ride from Moirans-en-Montagne on Monday.
Geraint Thomas was in prime position to win his maiden Tour de France after he retained the overall leader's yellow jersey in a lively 19th stage won by Slovenian Primoz Roglic as defending champion Chris Froome slipped down to fourth on Friday.
The 22-year-old Bernal, the youngest rider to win the race in 110 years, gave Team Ineos --formerly Team Sky -- their seventh title in the last eight editions.
Froome had been the favourite to retain his title but he paid the price for the efforts he made to win the Giro d'Italia in May as he just failed to become the first man in 20 years to achieve the Giro-Tour double.
Geraint Thomas tightened Team Sky's grip on the Tour de France when he handed the British outfit their sixth title in seven years on Sunday and there is no sign that their domination will end anytime soon.