Bagnaia broke the lap record set by Vinales in qualifying for the San Marino race in FP3 despite a fall and went into qualifying as the favorite after leading FP4.
Yamahas Vinales set the benchmark with 1: 31.647 minutes at the beginning of the second quarter, although FP3 pacesetter Bagnaia broke this with a new preliminary pole record of 1: 31.313 minutes on his Pramac Ducati.
Fabio Quartararo had jumped into second place on his Petronas Yamaha and was on course to drop Bagnaia when he wobbled while braking in the last corner.
Vinales jumped 1: 31.386 minutes ahead of Quartararo at the start of his second run, before beating Bagnaia’s time with 1: 31.268 on his follow-up tour.
Bagnaia lit the timing screens on his last attempt right at the end of the second quarter, completing the first lap of Misano under 1:31 minutes with a time of 1: 30.973 minutes.
However, this was scrubbed when he ran off the track from the final corner and was thrown back to fifth.
Vinales ended up shooting in 1: 31.077 seconds, which was good enough for second place, but he promoted him to pole when Bagnaia’s lap was canceled.
Pramac’s Jack Miller came through Q1 and jumped from 12th to second place in his last lap with 1: 31.153 minutes, while Quartararo completed the top 3 like a week ago.
Pol Espargaro jumped to fourth place on his KTM after his death, Bagnaia and Brad Binder’s sister-factory KTM completed the second row.
Espargaro’s late performance left Valentino Rossi in seventh place on his Yamaha, while San Marino winner Franco Morbidelli (Petronas) and Ducati’s Danilo Petrucci joined him in row three.
Andrea Dovizioso snuck into Q2 but only managed to finish 10th on his Ducati, while Suzuki’s Joan Mir took a disappointing 11th place ahead of Takaaki Nakagami – the LCR rider destroyed his second Honda in an accident at Turn 15 after he had done this in FP4.
A late improvement for Dovizioso in Q1 broke the hearts of Tech 3 and Iker Lecuona as he lost the rookie from Q2 spots right at the end of the session.
Lecuona had led the session with 1: 31.715 minutes after the first runs, but will start in the races on Sunday from an equally good 13th place in his career, ahead of Avintias Johann Zarco, who was not affected by a late fall in the Carro- Hairpin could recover.
Miguel Oliveira will start from 15th on the sister Tech 3 KTM while Aleix Espargaro lands in 16th on the Aprilia after falling late in Q1 while threatening to move him back to Q2 in one lap .
Suzuki’s Alex Rins was a mysterious 18th place who, at 1: 32.275 seconds behind Honda’s Alex Marquez, didn’t come close to Q2, with only Aprilia’s Bradley Smith and Avintia’s Tito Rabat being slower than Rins.