Update from Aprilia: 'During this morning's MotoGP Warmup, Maverick’s Aprilia just had an oil overflow. Nothing was broken, in fact the smoke was brief and he’ll actually race with the exact same bike.'
Vinales was shown the back and orange flag during Sunday morning warm-up after a cloud of smoke was emitted from his Aprilia.
While Vinales promptly responded by backing off, pulling wide and looking down at his bike, the smoke had stopped and he appeared to be asking what the flag had been for.
The Spaniard then continued to ride the remainder of the lap slowly and off line until he reached the pits.
The FIM Stewards have punished Vinales with a three-place grid penalty for "not respecting the black flag with orange disk by not immediately leaving the track".
Bagnaia, who starts the race 14 points ahead of Jorge Martin, thus moves to pole position ahead of Johann Zarco, with Jack Miller moving up to the front row in third.
Vinales now heads row two in fourth, followed by KTM's Brad Binder and Pramac Ducati's Sprint winner Martin.
Vinales joined Bagnaia in choosing the medium rear tyre (instead of the soft) for Saturday's Sprint and - after leading for six laps - dropped back to fourth place, with Bagnaia in fifth.