Jorge Lorenzo has broken his own qualifying lap record to secure pole for the San Marino MotoGP while Jack Miller was next-best.

Marc Marquez will start from the middle of the second row after a crash on his second run before he still briefly threatened to snatch pole.

The Repsol Honda rider rolled out the fastest lap of the weekend straight off the bat with a 1:32.016s before Lorenzo bettered the fastest ever lap at Misano by clocking a 1:31.763s.

Miller was third-fastest as those three ended their opening runs with just one lap on the board.

While Lorenzo didn’t set a time on his second run, Miller found more than four tenths of a second on his Pramac Ducati GP17 to take up second position with a 1:31.916s.

That lap came moments after Marquez went down at Turn 15, but with his first bike ready again for a two-stop strategy he was able to get a lift back to the pits and resume qualifying.

The championship leader looked like he might pull it out of the fire completely as he then set what be the fastest first sector, but his full-lap pace wasn’t good enough to improve.

Lorenzo, on the other hand, went quicker again with a 1:31.629s on the #99 Ducati Team entry to finish qualifying 0.287s clear of the field.

“A month ago, in the test, I set a (one minute-)31.9, so it was very difficult to improve the lap time, but all the riders in the qualifying find more speed from nowhere, from all the braking and the lean angle and acceleration,” said the Spaniard.

“The lap times were impressive and this 31.6 is a great lap so I’m very proud of it and I’m very happy.”

Miller’s starting berth is his personal best in a session not affected by weather, having qualified on pole in Argentina in April on a drying track.

“I don’t know (how I did it); I just put my head down,” he said.

“We’ve had good speed all weekend but I had a couple of spills yesterday. In the morning, just pushing too hard on used tyres; and then in the arvo, I just couldn’t get the tyre to work and I was building up my pace and then it caught me out in the last corner.

“I can’t thank the team enough. Judging by FP4, we have good pace for the race as well on used tyre, both soft and medium, so I’m excited.

“I didn’t expect this but I’ll take it, that’s for sure.”

Earlier, Miller had only just achieved direct passage to Qualifying 2 when he was second-fastest on a damp track in Free Practice 3.

Andrea Dovizioso (Ducati Team) went third-fastest in the final minute of qualifying before Maverick Viñales (Movistar Yamaha) spoiled what would have been an all-Ducati front row after the chequered flag.

In sixth is Cal Crutchlow, who crashed his LCR Honda late in the piece and also during Free Practice 4.

Row 3 is Valentino Rossi (Movistar Yamaha), Danilo Petrucci (Pramac Ducati), and Johann Zarco (Tech3 Yamaha).

Alex Rins (Suzuki Ecstar) starts alongside the two Q1 graduates in Dani Pedrosa (Repsol Honda) and Franco Morbidelli (Marc VDS Honda).

Lights go out for Sunday’s 27-lap race at the Misano World Circuit Marco Simoncelli at 2200 AEST.

Qualifying: San Marino MotoGP