Di Giannantonio set a 1:46.156 with the chequered flag out to head up a front row which comprises three Italians from two teams from the same country, riding Ducati’s Bologna bullets.
Marco Bezzecchi was second-fastest and fellow Mooney VR46 Racing Team rider took third on the starting grid at the Autodromo Internazionale del Mugello.
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Johann Zarco will start fourth and Francesco Bagnaia fifth, while defending MotoGP world champion Quartararo will take sixth.
Aprilia Racing’s Aleix Espargaro, who had topped the free practice sessions, claimed seventh.
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Joining him on Row 3 will be Takaaki Nakagami (LCR Honda Idemitsu) and Pol Espargaro (Repsol Honda Team), while Enea Bastianini (Gresini Racing MotoGP) rounds out the top 10 on yet another Ducati.
Jorge Martin (Prima Pramac Racing) qualified 11th-fastest but is set to start 14th as a result of a grid penalty for irresponsible riding in FP3.
Di Giannantonio came through Q1, when the arrival of light rain spiced up proceedings, but it was clear by the end of that session that slick Michelin tyres had to be the choice for Q2 despite persistent showers.
That meant the battle for pole would be less about strategy and more about a straight fight to set the quickest pace in the hills of Tuscany.

Q2 was red flagged barely more than a minute in as a result of a scary crash for Marquez at Turn 2.
Despite having some knowledge of the conditions due to riding in Q1, the Spaniard highsided on his first lap out of the pits, virtually tearing the front wheel off his RC213V.
Marquez was able to walk away but his bike caught fire and fluid spilt onto the track, necessitating a stoppage so that the surface could be cleaned up.
He would later get back out on his second bike and set a personal-best lap time of 1:47.468, but will start 11th due to Martin’s penalty.
Later, it was was announced at a special press conference that the six-time MotoGP world champion will travel to the US on Tuesday (May 31) for surgery, though he will be competing in the race at Mugello on Sunday.
However, post-surgery, the Spaniard will take a short break from competitive action.
1. Fabio Di Giannantonio (Gresini Racing MotoGP) – 1:46.156
2. Marco Bezzecchi (Mooney VR46 Racing Team) + 0.088
3. Luca Marini (Mooney VR46 Racing Team) + 0.171
4. Johann Zarco (Prima Pramac Racing) + 0.227
5. Francesco Bagnaia (Ducati Lenovo Team) + 0.315
6. Fabio Quartararo (Monster Energy Yamaha MotoGP) + 0.350
7. Aleix Espargaro (Aprilia Racing) + 0.351
8. Takaaki Nakagami (LCR Honda Idemitsu) + 0.405
9. Pol Espargaro (Repsol Honda Team) + 0.511
10. Enea Bastianini (Gresini Racing MotoGP) + 0.523
The lights glow off for the Italian GP at 2pm local time on Sunday (5.30pm IST). Indian audience can catch all the action live on Eurosport channel.
(By a special arrangement with Dorna Sports)
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