Vinales scored his first pole as an Aprilia rider and first since Assen 2021 on Saturday at the Ricardo Tormo Circuit with a new lap record.
The Aprilia rider rued his medium rear tyre choice, however, and dropped to fourth having led briefly during the 13-lap race.
In the 10-minute warm-up session on Sunday morning, Vinales was shown the black-and-orange flag after his RS-GP developed a problem.
Under the regulations, a rider must immediately pull off track once they see the flag.
But Vinales decided to ride back to his pit box instead, which was put under investigation by the FIM MotoGP stewards.
They determined that Vinales broke the rules and have imposed a three-place grid penalty on the Spaniard for the grand prix on Sunday afternoon.
Vinales will drop to fourth, which crucially promotes championship leader Bagnaia to pole for this afternoon’s title showdown with Jorge Martin.
Bagnaia leads Martin by 14 points coming into the finale after Martin took his ninth sprint win of the season on Saturday.
Martin qualified sixth and will stay there despite Vinales’ penalty, though does promote his Pramac team-mate Johann Zarco to second alongside Bagnaia.
For Bagnaia to win a second world championship, he needs to finish a minimum of fifth regardless of where Martin is to seal the deal.
Bagnaia said his sprint was compromised by his rear tyre choice, having opted for the medium, while Martin admitted he didn’t have a good front-end feeling on his charge to victory.
Both riders come into the season finale carrying warnings for breaking the minimum tyre pressure rules at the Thailand and Malaysian GPs respectively.
Should either of them break the rule again, they will be slapped with a three-second penalty, leading to fears by some riders in the paddock that the championship could be decided because of this.
In the sprint, Luca Marini and Franco Morbidelli were given three-second penalties for riding under the minimum front tyre pressure.
Vinales’ penalty promoted KTM’s Jack Miller onto the front row in third.
