Martin, who leads the championship by 39 points coming into the Mugello round, scored his third pole of the year with a new lap record of 1m44.504s set on his first flying lap.
The Spaniard, who looks set to step up to the factory Ducati team in 2025, beat reigning champion and last year’s Italian GP winner Bagnaia.
The Italian was just 0.043 seconds behind Martin, though will have to drop three grid spots for the grand prix after impeding Alex Marquez in practice on Friday afternoon.
Maverick Vinales completed the top three on his factory Aprilia, while Marc Marquez scored his best qualifying result since he was on pole at Jerez despite crashing late on in Q2.
The lap record was already beaten in the Q1 session by Pramac Ducati rider Franco Morbidelli, who topped that 15-minute segment with a 1m44.726s.
Team-mate Martin, on his first flying lap, lit up the timing screens at the start of Q2 and produced a 1m44.504s.
But Martin would never better this across the rest of the session and came under fire as the session wound down.
Bagnaia came close and was up on Martin through the first three sectors of his best lap, but lost out in the final split and came up just short with a 1m44.547s.
The factory Ducati rider will start second for Saturday’s sprint race, but for the grand prix he will be demoted to fifth.
Bagnaia was seething in parc ferme about this punishment, calling it a “clown penalty”.
“It’s one of the greatest thing I could do today, starting on the front row, because this clown penalty is something useless,” he said.
“But in any case, today it will be important to start well, to do the maximum. We know that our pace is very, very fast. So, I know if I can be leading in the first laps we can have a good advantage.”
Aprilia’s Vinales put together a good final lap, but also lost out in the final sector and had to settle for third.
Gresini Ducati’s Marc Marquez looked like he was on course to beat Martin’s time with just under three minutes to go in Q2, but crashed going into Turn 10.
Despite this, Marquez held onto fourth in his first Q2 appearance since the Spanish GP and will be promoted to the front row for the grand prix courtesy of Bagnaia’s podium.
Enea Bastianini was fifth on the second factory team Ducati ahead of Q1 pacesetter Morbidelli, while Tech3 rookie Pedro Acosta headed row three in seventh on the sole KTM in Q2.
Alex Marquez was eighth on his Gresini Ducati, with Aleix Espargaro (Aprilia) and Yamaha’s Alex Rins completing the top 10. Trackhouse Aprilia duo Miguel Oliveira and Raul Fernandez capped off row four.
KTM’s Brad Binder couldn’t lift himself out of Q1 and will start 13th, while Fabio Quartararo couldn’t scale the same heights as his Yamaha team-mate Rins down in 15th.
Joan Mir was the fastest Honda in 17th.
MotoGP Italian GP – Q2 results:
