Lotus are expected they will continue with Jarno Trulli and Heikki Kovalainen as drivers in 2011.
Kubica's team-mate Nick Heidfeld and the second Toyota of Jarno Trulli completed the top 10.
BBC: Hamilton edged out Ferrari's Kimi Raikkonen by 0.102secs
Jarno Trulli, who Fisichella has replaced, scored Renault's one win last year in Monaco.
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Toyota's Jarno Trulli was delighted he could hold out Hamilton to claim fourth place.
Trulli said he used the above to ensure he was mentally prepared for a race.
"I am happy because I wanted some justice and I got it, " said Trulli.
That was the case at a recent dinner with friends at I Trulli restaurant in New York.
WSJ: Second Thoughts: How to Follow Your First Bottle | On Wine by Lettie Teague
"We could not have expected to be here when we stated our relationship with Toyota, " said Trulli.
Both Trulli and Alonso were realistic about their chances of converting excellent qualifying runs into podium places.
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Jarno Trulli ran off the circuit, Hamilton passed him and then allowed the Toyota man to re-pass him.
Driver Jarno Trulli said Toyota were "better prepared than ever" and "ready to face the fight for 2009".
Trulli, meanwhile, is hoping Toyota can finally convert their large investment off the track to success on it.
Alonso heads into Renault's home Grand Prix on the second row of the grid along with Toyota's Jarno Trulli.
Juan Pablo Montoya was a distant third for Williams, ahead of the Renaults of Fernando Alonso and Jarno Trulli.
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He shrugged off suggestions that the absence of Trulli, who is good friends with Alonso, would disrupt team harmony.
Force India's Adrian Sutil and Toyota's Jarno Trulli make up the second row.
He seized first place from Toyota's Jarno Trulli at the third time of asking, setting a benchmark of 1:12.353.
Trulli and Toyota have been reinstated to third, and McLaren will not appeal.
Red Bull's Sebastian Vettel was second from Toyota's Jarno Trulli as Hamilton had his best finish of 2009 in fourth.
The Finn, who joins Jarno Trulli in the Norfolk-based team, has had his seat fitted at the team's Hingham factory.
Italian Jarno Trulli took sixth place for Toyota ahead of the third championship contender, Sebastian Vettel, in the second Red Bull.
With Glock passing pole-sitter Trulli off the line for the lead, Hamilton rocketed into third, with Button also slipping ahead of Vettel.
Malaysian Fairuz Fauzy will take part in first practice in Hockenheim for Lotus in place of either Jarno Trulli or Heikki Kovalainen.
He did, though, make up enough ground to emerge ahead of Trulli.
The Englishman was himself some way ahead of the Williams of Kazuki Nakajima, with Jarno Trulli's Toyota taking the final points position.
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With Ralf Schumacher following his brother Michael into retirement, Jarno Trulli assumes the lead driver position in his fourth season at Toyota.
Coulthard moved up to second at Hockenheim after Michael Schumacher suffered a late-race puncture shortly after both men had passed Jarno Trulli's Renault.
Just then, I Trulli's owner and wine director, Nicola Marzovilla, appeared.
WSJ: Second Thoughts: How to Follow Your First Bottle | On Wine by Lettie Teague
Toyota's Jarno Trulli was also upbeat about his team's progress.
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