Raikkonen again suffered the heartbreak of retiring while leading.
Ferrari's world champion Michael Schumacher, winner at Silverstone last year, qualified a disappointing ninth.
The 23-year-old Spaniard lapped the Magny-Cours circuit in one minute 14.412 seconds for his third pole in 10 races this season.
McLaren's Spanish test driver Pedro de la Rosa, who will not compete on Sunday, was the fastest but it was Renault's championship leader and compatriot Fernando Alonso who came closest to his time.
Formula One leader Max Verstappen passed Mercedes rival Lewis Hamilton on the penultimate lap to win a tense French Grand Prix for Red Bull on Sunday and canter 12 points clear at the top.
Race leader Kimi Raikkonen crashed out with one lap remaining.
Renault's championship leader Fernando Alonso finished second ahead of Italian Jarno Trulli in a Toyota.
"He's got the old matador spirit, that's for sure."
Renault announced the Formula One comeback of Danish driver Kevin Magnussen at the launch on Wednesday of a new-look team that will put the French carmaker back on the starting grid as a constructor.
Nobody leaving Imola could doubt that the battle lines were drawn for what promises to be a thrillingly competitive season.
Jordan's Indian ace posted his third finish in four races in the Formula One championship.
The 21-year-old Alonso has a star quality like no other Spaniard in Formula One since the 1950s.
Fernando Alonso reiterated his long-term love and loyalty to Ferrari on Friday after McLaren, the Formula One team he left in acrimonious circumstances in 2007, said they would be keen to sign him.
Jarno Trulli was second for Toyota, while Michael Schumacher took third place in the new F2005 in the first qualifying for the Bahrain Grand Prix.
Jaguar team boss Tony Purnell feels the Australian driver is a world champion in the making.
The Dutchman stopped Hamilton from winning an eighth title with a gutsy turn in the final lap.
Fernando Alonso indicated his Formula One future was in his own hands despite Red Bull announcing on Saturday that four time world champion Sebastian Vettel was leaving to join Ferrari.
The reigning World champion gave his new Ferrari a winning debut in Spain on Sunday as title leaders McLaren were reduced to mere spectators.
Sebastian Vettel's hopes of fighting champions Mercedes for victory in Sunday's Bahrain Formula One Grand Prix went up in smoke before the start when his Ferrari's engine blew on the formation lap.
"I think he is in the perfect position. Honestly, he has a strong car, they're very quick, very consistent," Schumacher said.
Seven-times world champion Lewis Hamilton became the first Formula One driver to take 100 pole positions after lapping fastest for Mercedes in Spanish Grand Prix qualifying on Saturday.
Seven-time world champion Lewis Hamilton overtook main rival Max Verstappen and Mercedes team mate Valtteri Bottas to win the Portuguese Grand Prix on Sunday and go eight points clear in the Formula One standings.
Lewis Hamilton believes Charles Leclerc has usurped four times world champion team mate Sebastian Vettel as Ferrari's favourite.
Sebastian Vettel cruised to a third straight Singapore Grand Prix victory on Sunday and moved closer to a fourth consecutive Formula One world title with a dominant drive under the floodlights at the Marina Bay Street Circuit.
Sebastian Vettel continued his imperious march towards a fourth consecutive Formula One world championship by storming to pole position at the Singapore Grand Prix on Saturday after dominating the two days of practice.
'I appreciate the quest for safety but this is Formula One and the way it is now is perfectly fine' 'I am sad for the sport... it doesn't look right from outside when in one week we change the qualifying format three times'
Unlike the Australian GP, where the majority of drivers carried out only one pit-stop, of Sunday's second race of the season, at Sepang, Malaysia, will see at least two, says Raja Sen.
Kimi Raikkonen will race for Ferrari next season after agreeing a two-year deal that takes the 2007 Formula One World champion back to the glamour team he left in 2009.
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