Daniel Ricciardo finished third for McLaren ahead of teammate Lando Norris, who kept Hamilton in check for the duration of the race disrupted by an accident on the first lap of 2020 Monza winner Pierre Gasly.
The result means that Verstappen will start the Grand Prix on Sunday from the front, with Ricciardo at his side in the front row, as Bottas will fall back to the bottom of the field before qualifying on Friday evening for a fresh Mercedes engine.
At the start, Bottas led slightly away from pole, followed by Verstappen as Hamilton’s slow escape meant that he was forced to defend Norris’ run into the first corner.
The world champion was then run over by Ricciardo and Gasly on his left and as the field closed for the first turns, Hamilton was squeezed behind the AlphaTauri and Norris on his right to drop to fifth through the exit from Turn 2 .
When Bottas, Verstappen and Ricciardo ran flawlessly through the long Curve Grande, Gasly, who briefly tagged the left rear wing of the McLaren and damaged his front wing, shot into the gravel when his wing broke apart and went under the front wheels.
Gasly slid over the gravel outside and hit the barriers, bouncing back into the gravel before stopping where the Frenchman got out.
The incident meant that the safety car was called – shortly after a collision between Yuki Tsunoda and Robert Kubica swung it around between the two tips of the chicane della Roggia – when Gasly’s car was recovered.
The race was restarted on lap four of 18, Bottas cavorting 1.6 seconds ahead of Verstappen, with Hamilton chasing the two McLarens – both on the soft tires against the middle ones on the two leaders and the second Mercedes.
When Norris held Hamilton in check, even though DRS was activated at the beginning of the sixth round, Ricciardo quickly fell away from Bottas and Verstappen.
The leaders were the only drivers able to complete a lap on lap 1:23, and on lap 10 they were over five seconds ahead of Ricciardo.
Bottas and Verstappen exchanged the fastest laps, but Mercedes never seemed to be in danger as the gap fluctuated from the two-second mark every now and then and approached the two-thirds finished mark.
The leading duo continued to break away from Ricciardo for the rest of the race, with Bottas in the lead – and finally won by 2.3 seconds.
Ricciardo crossed the finish line 14.5 seconds behind the winner, Norris defied Hamilton, who at times slipped dramatically in the wake of his compatriot, to the flag, where Hamilton landed 20 seconds behind his victorious teammate.
Charles Leclerc led his Ferrari team-mate Carlos Sainz home in sixth and seventh – the former recovered from his discomfort at the end of FP2 to start the sprint race from eighth, where he entered the first lap in hand-to-hand combat got out of the first corners.
Sainz, whose Ferrari was hastily rebuilt after his severe FP2 crash at Ascari, came home from where he started and in front of Antonio Giovinazzi.
The Alfa Romeo driver held the onrushing Sergio Perez back to the finish, while the Red Bull driver was embroiled in the other main focus of the race – his attempts to overtake Aston Martin’s Lance Stroll on lap nine.
After Perez attacked outside of Turn 1, Perez crossed the raised curbs in the runoff behind it and stayed ahead as the pair sped towards Curve Grande.
Red Bull ordered him to give the place back, which he did on the same lap at Ascari, and on the next tour, Perez made a similar move at Turn 1 to get ahead of Stroll and then begin his ultimately unsuccessful pursuit of Giovinazzi.
Stroll was 10th ahead of Fernando Alonso and Sebastian Vettel.
Tsunoda pitted after his encounter with Kubica and reclaimed 16th place, with Kimi Raikkonen’s temporary replacement at Alfa Romeo coming home 18th among the Haas cars as Gasly was the only retirement of the race.
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