Lost the front
At the beginning it was Marquez who led the field over the line and set the first benchmark; a 2:13.641 to edge out Jack Miller (Alma Pramac Racing), who was just behind the Spaniard on track.
The Repsol Honda rider then lost the front at Turn 4, however, and there was no saving this one.
Zarco put in a personal best lap to re-take P2 from ‘The Doctor', but the gap between the number 93 and his rivals remained 0.548 after a masterclass from Marquez for his 80th career pole position across all classes.
Then, though, news came through of the penalty and although it remains a Marquez pole in the statistics, he'll be starting seventh.
That means Dovizioso starts fourth despite his crash, with fellow Desmosedici rider Miller ending the session P6 after setting his best lap on his final lap.
He now starts in the middle of a second row completed by teammate Danilo Petrucci. Marquez heads Row 3, ahead of Friday's quickest rider Alex Rins (Team Suzuki Ecstar) and Q1 graduate Alvaro Bautista (Angel Nieto Team.
Dani Pedrosa (Repsol Honda Team), Australian GP winner Maverick Vinales (Movistar Yamaha MotoGP) and Aleix Espargaro (Aprilia Racing Team Gresini) line up on a super-powered Row 4.
The MotoGP race starts at the earlier time of 13:00 local time (10.30 am IST) after changes to the schedule.