Reigning world champion Marquez crashed heavily in last week’s Spanish GP and was set to miss this weekend’s second Jerez race following surgery on Tuesday.
However, he was declared fit to ride on Thursday by MotoGP’s medical team, though as a compromise with Honda, Marquez sat out Friday’s action as a precaution.
Completing 18 laps across the 45-minute session, Marquez will face Q1 later this afternoon, though was only 1.2 seconds off the best pace and just eight tenths from the top 10.
The slightly cooler conditions relative to FP2 meant improvements on the combined times as the field placed their bids for automatic Q2 graduation were immediate, with LCR Honda’s FP2 pacesetter Takaaki Nakagami moving up to third overall with a 1m37.235s.
Spanish GP race winner Fabio Quartararo also leapt up to fifth in the combined standings, having focused almost exclusively on race set-up on Friday.
Yamaha’s Vinales’ best time from Friday was finally toppled with 27 minutes remaining as Pramac Ducati’s Francesco Bagnaia took over top spot with a 1m36.847s.
This stood for around six minutes, before Quartararo smashed his own lap record from qualifying last week with a 1m36.643s on his Petronas Yamaha.
That lap stood until the final minute, when Vinales edged ahead by 0.059s with a 1m36.584s.
Pramac’s Jack Miller leapt up to third late on with a 1m36.710s to trail the Yamaha duo, with Nakagami holding onto fourth as top Honda runner ahead of Bagnaia.
Danilo Petrucci produced a 1m36.937s late on to move into sixth, while his factory Ducati teammate Andrea Dovizioso missed the Q2 cut by two tenths down in 14th.
KTM rookie Brad Binder bagged a place in Q2 for the first time in seventh, beating the second works Yamaha of Valentino Rossi and his factory KTM teammate Pol Espargaro.
Joan Mir grabbed the last direct Q2 place on his Suzuki in 10th, with Aprilia’s Aleix Espargaro being nudged out by just 0.017s after a second fall at Turn 2, having crashed earlier at Turn 6.
Franco Morbidelli (Petronas), Tech 3 KTM's Miguel Oliveira, Avintia Ducati’s Johann Zarco and Alex Marquez on the factory Honda will join Dovizioso and Marquez in Q1.
Cal Crutchlow found over a second from his Friday best in 17th on the LCR Honda as he grits his teeth through a recently operated on fractured wrist.
Alex Rins sat out FP3 as he struggles with the shoulder he fractured and dislocated last week, but the Suzuki rider's intention is to ride in FP4 ahead of qualifying.
|1||12|| Maverick Viñales ||Yamaha||1'36.584|
|2||20|| Fabio Quartararo ||Yamaha||1'36.643||0.059|
|3||43|| Jack Miller ||Ducati||1'36.710||0.126|
|4||30|| Takaaki Nakagami ||Honda||1'36.842||0.258|
|5||63|| Francesco Bagnaia ||Ducati||1'36.847||0.263|
|6||9|| Danilo Petrucci ||Ducati||1'36.937||0.353|
|7||33|| Brad Binder ||KTM||1'36.938||0.354|
|8||46|| Valentino Rossi ||Yamaha||1'36.988||0.404|
|9||44|| Pol Espargaro ||KTM||1'36.995||0.411|
|10||36|| Joan Mir ||Suzuki||1'37.053||0.469|
|11||41|| Aleix Espargaro ||Aprilia||1'37.070||0.486|
|12||21|| Franco Morbidelli ||Yamaha||1'37.180||0.596|
|13||88|| Miguel Oliveira ||KTM||1'37.278||0.694|
|14||4|| Andrea Dovizioso ||Ducati||1'37.295||0.711|
|15||5|| Johann Zarco ||Ducati||1'37.304||0.720|
|16||73|| Alex Marquez ||Honda||1'37.557||0.973|
|17||35|| Cal Crutchlow ||Honda||1'37.621||1.037|
|18||53|| Tito Rabat ||Ducati||1'37.828||1.244|
|19||93|| Marc Marquez ||Honda||1'37.882||1.298|
|20||38|| Bradley Smith ||Aprilia||1'38.016||1.432|
|21||27|| Iker Lecuona ||KTM||1'38.360||1.776|
|22||42|| Alex Rins ||Suzuki|
|View full results|