Jorge Lorenzo set a new track record to snatch pole position for Sunday's San Marino MotoGP ahead of Australian Jack Miller and fellow Spaniard Maverick Vinales.
World champion and current championship leader Marc Marquez of Honda suffered a shock fall that resulted in last year's winner qualifying fifth on a spare bike.
Three-time top-class world champion Lorenzo dominated Saturday's second qualifying session to claim his third pole so far this season with a record time of 1min 31.629sec around the Misano track.
The 31-year-old from Majorca, who also took pole for the British Grand Prix which was cancelled two weeks ago because of torrential rain, bettered his own previous Misano lap record from last year.
Lorenzo -- a three-time winner in Misano -- finished 28 hundredths of a second ahead of Alma Pramac Racing's Miller with Yamaha's Vinales at 0.32sec.
Lorenzo's Ducati teammate Andrea Dovizioso and Marquez closed out the top five, ahead of Britain's Cal Crutchlow, of Honda, who also crashed.
Italy's Valentino Rossi was seventh fastest for Yamaha, at a venue where he has won three times - most recently in 2014.
In recent years, Spaniards have dominated at the track on Italy's Adriatic coast, not far from the tiny republic from which the race takes its name.
The 25-year-old Marquez has won twice in the past three years for Honda.
Marquez has suffered a two-race blip, but so dominant is the Spanish world champion that he still increased his lead in the MotoGP standings without winning.
With seven races to go, Marquez is 59 points ahead of Rossi. Lorenzo and Dovizioso, who took the other podium places in the last two races, are 12 and 13 points further back.
Italian Francesco Bagnaia of the Sky Racing Team took pole in the Moto2 category and Spaniard Jorge Martin leading Moto3 on his Honda.