Under cloudy skies, Q2 for the French MotoGP got underway on Saturday afternoon with Cal Crutchlow on the soft front tyre posting a 1:34.084 to lead the way.
Jorge Lorenzo slotted into second place, 0.063s down, while Bradley Smith was third in the early running.
It was all-change, though, as Marquez crossed the line with a 1:33.374 while his Honda team-mate Dani Pedrosa, contesting his first MotoGP weekend after undergoing surgery on an arm pump problem, slotted into second.
But the grid for Sunday's race was by no means decided.
Lorenzo hit the front before being overhauled by Andrea Iannone only for Marquez to fight back with a 1:32.983. That time, though, was still 0.9s off his pole time from a year ago.
With five to go they were the provisional front row while a disgruntled Valentino Rossi was down in 12th place. The Championship leader was 1.541s off the pace.
Heading back out onto the track with fresh rubber, Marquez lowered his P1 time to a 1:32.246 while Andrea Dovizioso shot up to second place, 0.503s slower than Marquez. Lorenzo upped his pace but had to settle for third, 0.600s down to complete the front row of the French grid.
Crutchlow finished an impressive fourth for LCR Honda , ahead of Iannone and Smith. Rossi recovered to seventh place while Pedrosa was P8.
Marquez heads into Sunday's race fourth in the riders' standings, 26 points behind Rossi.
Earlier Q1 took place on a fast drying Le Mans circuit with Danilo Petrucci and Aleix Espargaro – cleared to ride despite suffering pain in his back and hand following a monster high-side earlier in the day – the two riders to progress.
Petrucci ultimately qualified P9 with Esparago tenth.
1 Marc MARQUEZ Repsol Honda Team 1'32.246
2 Andrea DOVIZIOSO Ducati Team 1'32.749 0.503
3 Jorge LORENZO Movistar Yamaha 1'32.846 0.600
4 Cal CRUTCHLOW CWM LCR Honda 1'32.897 0.651
5 Andrea IANNONE Ducati Team 1'33.001 0.755
6 Bradley SMITH Monster Yamaha Tech 3 1'33.299 1.053
7 Valentino ROSSI Movistar Yamaha MotoGP 1'33.352 1.106
8 Dani PEDROSA Repsol Honda Team 1'33.419 1.173
9 Danilo PETRUCCI Pramac Racing 1'33.556 1.310
10 Aleix ESPARGARO Team SUZUKI ECSTAR 1'33.665 1.419
11 Yonny HERNANDEZ Pramac Racing 1'33.714 1.468
12 Pol ESPARGARO Monster Yamaha Tech 3 1'33.724 1.478
13 Maverick VIÑALES Team SUZUKI ECSTAR 1'34.245
14 Nicky HAYDEN Aspar MotoGP Team 1'34.267
15 Scott REDDING EG 0,0 Marc VDS 1'34.551
16 Stefan BRADL Athinà Forward Racing 1'34.575
17 Mike DI MEGLIO Avintia Racing 1'34.833
18 Jack MILLER CWM LCR Honda 1'34.858
19 Hector BARBERA Avintia Racing 1'34.870
20 Karel ABRAHAM AB Motoracing 1'34.940
21 Eugene LAVERTY Aspar MotoGP Team 1'34.947
22 Loris BAZ Athinà Forward Racing 1'35.456
23 Alvaro BAUTISTA Aprilia Racing Team Gresini 1'35.458
24 Alex DE ANGELIS Octo IodaRacing Tea 1'35.680
25 Marco MELANDRI Aprilia Racing Team Gresini 1'37.522