The factory Aprilia rider put in the first ever 1m28s lap at Circuit Ricardo Tormo with a 1m28.931s to take his first pole since Assen in 2021, two days prior to announcing he was quitting Yamaha a year early.
He led from factory Ducati rider Bagnaia, who dominated Q1 before finishing Q2 in second, while title rival Jorge Martin finished just sixth for Pramac.
Pramac’s Johann Zarco will line up third in his final race with the Ducati satellite team before moving to LCR Honda next season.
It hands Bagnaia the advantage heading into this afternoon’s sprint race, where he can clinch his second consecutive title if he outscores Martin by four points.
Martin narrowly escaped disaster at the start of Q2 after Marc Marquez’s tear off nearly got caught in his airbox, with the Pramac rider quickly stopping the offending debris with his hand.
Vinales took an early lead with a 1m29.534s after the first laps, before he was bettered by factory KTM rider Brad Binder, with Martin second and Bagnaia last.