The battle for pole position was started by Maverick Viñales, who, by the way, set the first target time with a rear spoiler on his Aprilia RS-GP and went down to a 1:31.120 min in the next two laps.
Repsol Honda factory rider Marc Márquez proved he could be quick without a driver, moving into provisional second place just 0.084s behind Viñales at the halfway point in the 15-minute session.
When the MotoGP aces then left the pit lane for their second Q2 run with fresh tires, Viñales of all people had to push his RS-GP back into the pits, apparently due to an electronic problem.
It was even worse for Aprilia: Aleix Espargaró crashed heavily in the first corner, looked bruised at first, but then got back up, but his qualifying ended early.
With a minute to go, Pramac ace Jorge Martin and just behind him even quicker Marc Márquez beat the Viñales time. Red Bull KTM factory rider Jack Miller pushed ahead of Martin shortly afterwards.
In the finish, Bagnaia snatched the supposed pole position from Márquez with a perfect last sector. VR46 Ducati protégé Luca Marini made it into the front row of the grid in the slipstream of the world champion after a detour via Q1.
Fabio Quartararo, on the other hand, only witnessed the decisive second qualifying session at his home GP as a spectator: The Yamaha star got stuck behind the sensational rookie Augusto Fernández in Q1, starting from 13th on the grid, the starting position of the Frenchman is difficult.
The Bavarian Jonas Folger is on the second RC16 in the GASGAS Tech3 colors on the 21st starting place.
MotoGP result Q2, Le Mans (05/13):
1. Bagnaia, Ducati, 1:30.705s
2. Marc Marquez, Honda, + 0.058 sec
3.Marini, Ducati, +0.137
4.Miller, KTM, +0.279
5. Martin, Ducati, +0.318
6. Vinales, Aprilia, +0.415
7. Bezzecchi, Ducati, +0.468
8. Alex Marquez, Ducati, +0.570
9. Zarco, Ducati, +0.593
10. Brad Binder, KTM, +0.740
11. Aleix Espargaró, Aprilia, +0.818
12. Augusto Fernandez, KTM, +0.891
The rest of the starting lineup:
13. Quartararo, Yamaha, 1:31.366 mins
14. Nakagami, Honda, 1:31.545
15. Di Giannantonio, Ducati, 1:31.718
16. Mir, Honda, 1:31.810
17. Morbidelli, Yamaha, 1:31.886
18. Rins, Honda, 1:31.959
19.Petrucci, Ducati, 1:32.092
20. Savadori, Aprilia, 1:32.410
21. Folger, KTM, 1:33.605
MotoGP result FP, Le Mans (13.05.):
1. Vinales, Aprilia, 1:31.898 minutes
2. Bagnaia, Ducati, + 0.293 sec
3.Miller, KTM, +0.357
4. Marc Marquez, Honda, +0.491
5. Aleix Espargaró, Aprilia, +0.551
6. Morbidelli, Yamaha, +0.630
7. Martin, Ducati, +0.686
8. Zarco, Ducati, +0.694
9. Quartararo, Yamaha, +0.702
10.Marini, Ducati, +0.736
11. Augusto Fernandez, KTM, +0.741
12. Di Giannantonio, Ducati, +0.773
13. Mir, Honda, +0.897
14. Nakagami, Honda, +0.924
15. Alex Marquez, Ducati, +0.988
16. Brad Binder, KTM, +0.996
17. Rins, Honda, +1.135
18.Petrucci, Ducati, +1,440
19. Follower, KTM, +2,322