Miller left it late to secure a clean sweep on Friday at Le Mans, putting in a 1m30.950s to lead Aprilia's Espargaro by 0.119 seconds on his final lap of the session.
Despite the threat of rain looming over a grey Le Mans, all riders were able to improve on their FP1 times as they vied for a place directly into Q2 for Saturday's qualifying session.
For now, that session won't feature 2021 world champion Quartararo, with the Yamaha rider only 12th at the chequered flag and into Q1.
Having crashed on his comeback from injury on Friday morning, Marquez ended the day with a big off at Turn 9 on his final flying lap and wrecked his Honda.
The session started with several crashes in quick succession, with Espargaro, RNF Aprilia stand-in Lorenzo Savadori, Tech3 GASGAS' Augusto Fernandez and Alex Marquez on the Gresini Ducati taking tumbles inside the first 15 minutes of FP2.
After 15 minutes of running, the most significant lap time improvement came from VR46 Ducati's Marco Bezzecchi, who moved up to third overall with a 1m31.654s having ended FP1 eighth.
With around 20 minutes of the hour-long session remaining, Yamaha's Quartararo took to his home track kitted out with fresh soft rubber to begin the time attack phase of the afternoon.
On his first two laps, the Frenchman ran wide at the downhill Turn 6 right-hander as he continued to search for more feeling from the front end of his Yamaha.
Quartararo's third flying lap of that run produced a 1m31.675s to go eighth-fastest, while moments later Brad Binder on the factory KTM went top with a 1m31.352s.
Miller deposed his team-mate with a 1m31.312s with 10 minutes to go, though only briefly stood at the top of the timesheets as Bezzecchi took over with a 1m31.150s.
With two minutes to go, Aprilia's Espargaro went fastest with a 1m31.069s – but would have to settle for second after Miller's 1m30.950s final effort.
Bezzecchi completed the top three from Pramac duo Jorge Martin, who crashed early in the session, and Johann Zarco.
Maverick Vinales was sixth on his factory Aprilia from Binder and Marc Marquez, who made it into Q2 directly despite his fall at the end of the session.
Reigning world champion Francesco Bagnaia was ninth on his factory Ducati ahead of Gresini's Alex Marquez, while Luca Marini was shuffled out of the top 10 by 0.003s on his VR46 Ducati.
He will face Q1 on Saturday morning along with Quartararo, Honda's Joan Mir and LCR counterpart Alex Rins who were 13th and 14th.
| Cla | Rider | Bike | Laps | Time | Gap | |
|---|---|---|---|---|---|---|
| 1 |  Jack Miller |
 |
KTM | 27 | 1'30.950 | |
| 2 |  Aleix Espargaro |
 |
Aprilia | 23 | 1'31.069 | 0.119 |
| 3 |  Marco Bezzecchi |
 |
Ducati | 27 | 1'31.150 | 0.200 |
| 4 | Jorge Martin |
 |
Ducati | 17 | 1'31.235 | 0.285 |
| 5 |  Johann Zarco |
 |
Ducati | 24 | 1'31.276 | 0.326 |
| 6 | Maverick Viñales |
|
Aprilia | 28 | 1'31.342 | 0.392 |
| 7 |  Brad Binder |
 |
KTM | 22 | 1'31.352 | 0.402 |
| 8 | Marc Marquez |
 |
Honda | 26 | 1'31.432 | 0.482 |
| 9 | Francesco Bagnaia |
 |
Ducati | 23 | 1'31.467 | 0.517 |
| 10 | Alex Marquez |
 |
Ducati | 21 | 1'31.508 | 0.558 |
| 11 | Luca Marini |
 |
Ducati | 27 | 1'31.511 | 0.561 |
| 12 | Fabio Quartararo |
 |
Yamaha | 29 | 1'31.650 | 0.700 |
| 13 | Alex Rins |
 |
Honda | 27 | 1'31.942 | 0.992 |
| 14 | Augusto Fernandez |
 |
KTM | 23 | 1'31.990 | 1.040 |
| 15 |  Takaaki Nakagami |
 |
Honda | 27 | 1'31.998 | 1.048 |
| 16 | Franco Morbidelli |
 |
Yamaha | 18 | 1'32.143 | 1.193 |
| 17 | Fabio Di Giannantonio |
 |
Ducati | 24 | 1'32.311 | 1.361 |
| 18 | Joan Mir |
 |
Honda | 21 | 1'32.369 | 1.419 |
| 19 | Danilo Petrucci |
 |
Ducati | 23 | 1'33.022 | 2.072 |
| 20 | Lorenzo Savadori |
 |
Aprilia | 18 | 1'33.489 | 2.539 |
| 21 |  Jonas Folger |
 |
KTM | 25 | 1'33.672 | 2.722 |
| View full results | ||||||
