Vinales was on top for most of the session, reeling off times consistently quicker than his rivals before reaching a 1m43.696s.
Miguel Oliveira grabbed second for Mahindra late on and closed to within 0.110 seconds of Vinales, equalling his career best qualifying.
Jonas Folger completes the front row for Aspar.
The Monlau riders had to settle for fourth and seventh, with Alex Rins and Alex Marquez split by Luis Salom and Jack Miller.
That Salom was even taking part in qualifying was remarkable following a violent crash in final practice.
The Spaniard, currently second to Vinales in the standings, had to have an ultrasound scan on his kidneys before he was cleared to return to the track.
Another practice crasher, Efren Vazquez, was less fortunate. He sustained a broken collarbone on Friday and will not race.
- Sports & Recreation
- Luis Salom
- Alex Rins