Bagnaia had to beat Quartararo by three points to keep the championship alive and looked good to do so as he led the first 22 tours from pole while Quartararo advanced from 15th
But a late fall for the Ducati rider put an end to all his hopes, with fourth place more than enough for Quartararo to become France’s first MotoGP world champion at just 22 years old.
Bagnaia had the dream start from pole position to take the lead from his fast-starting Ducati team-mate Jack Miller, despite KTM’s Miguel Oliveira briefly finishing second.
Miller drove past the inside of Rio’s right-hand bend, while championship leaders Quartararo lost positions from 15th to 17th after the first few corners.
Marquez followed Miller to Oliveira in the Quercia left turn, with Miller now in a perfect position to act as Bagnaia’s rear gunner.
Both Ducatis opted for a late hard front tire change despite the cold conditions, and Miller crashed at Turn 15 on lap four when he stowed Marquez’s front defense.
At this point Quartararo had worked his way up to 12th place, while Marquez – just like last month in Aragon – built up the pressure on Bagnaia at the top, the gap between the leaders constantly fluctuating around the 0.2s mark.
The first two had Pol Espargaro, over two seconds behind third place, while Quartararo advanced to ninth place by the ninth lap.
Quartararo was much faster than the group of riders in front of him, and on lap 19 of 27 – after a brief battle with Aprilia’s Aleix Espargaro – the Yamaha rider was fifth.
That looked like it was the best Quartararo could hope for as Oliveira was fourth over eight seconds from the finish.
At the same time, Bagnaia’s pace proved too fast for Marquez and made his decisive break when a gap of almost a second opened between them on lap 23.
But Bagnaia’s authoritative drive ended at Turn 15 under the same circumstances as his teammate Miller when he lost the front of his Ducati.
This gave Marquez his third win of the season and the first Repsol Honda 1-2 in MotoGP since Aragon 2017, while Pol Espargaro was second for his first podium as an HRC rider.
Avintia’s Enea Bastianini stormed through from 16th on the grid on his two-year Ducati and grabbed Quartararo’s third place on the last lap of the Caro hairpin to claim his second MotoGP podium.
But fourth place was enough for Quartararo to become the first Yamaha rider to win the world championship since 2015.
Pramacs Johann Zarco completed the top 5 ahead of Suzuki’s Alex Rins, whose teammate Joan Mir dropped out early after a tangle for Danilo Petrucci after he had already been hit with a double long lap penalty for jump starts.
Aleix Espargaro ended up losing to Aprilia teammate Maverick Vinales in seventh place, while Avintias Luca Marini led his brother Valentino Rossi, with the Petronas SRT rider finishing in the top 10 on his last MotoGP appearance in Italy.
Brad Binder recovered from a lap accident on his KTM and finished 11th ahead of Ducati Wildcard Michele Pirro, Andrea Dovizioso from SRT, Franco Morbidelli from Yamaha and Takaaki Nakagami from LCR after an early crash.
Oliveira was late, Pramacs Jorge Martin, Tech 3s Iker Lecuona and LCRs Alex Marquez also failed.