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.
Source: Autosport