Danilo Petrucci topped a damp MotoGP FP3 for the Valencia Grand Prix with the best time of the weekend, while both factory Yamahas will contest Q1 this afternoon, with Valentino Rossi crashing early on.
Rain began to fall just as the session got underway, with Pramac's Danilo Petrucci setting a benchmark of 1:42.904s instantly beaten by Rossi with a 1:42.600s.
Marquez soon deposed the Italian, while Johann Zarco moved his Tech3 Yamaha ahead of the works M1 rider 0.041s behind Marquez.
Rossi returned to the top of the standings with a succession fastest laps, culminating in a 1:41.569s, though remained 12th on the combined standings.
The Italian's hopes of making it into the Q2 progression places took a knock when he was flicked from his Yamaha at Turn 4, though he soon returned to the action having walked away from the crash unscathed.
Marquez re-established top spot with just under 15 minutes of the session gone, deposing brief leader Andrea Dovizioso [Ducati] with a 1:40.871s, before proceeding to move the goalpost even more with a 1:40.086s to go eight tenths clear of the field.
With half the 45-minute session gone, only Zarco and Yamaha stablemate Maverick Vinales had improved overall on the timesheets inside the top 10 in sixth and seventh respectively, while Marquez's 1:39.767s from FP1 still stood as the reference.
On the individual timesheet, Petrucci returned to the top of the pile, usurping Marquez by 0.054s as FP3 entered its final quarter.
A 1:39.800s from Dovizioso moved him up to second overall on the timesheets and top of FP3, before Petrucci fired in a 1:39.712s in the dying stages to go fastest on the combined times.
Petrucci remained unchallenged and heads to qualifying as the rider to beat, while Marquez remains ahead of Dovizioso on the combined standings despite the Ducati ruder edging him by 0.086s in FP3.
A late fall for Pramac's Jack Miller did not stop him from securing a place in Q2, with Zarco heading Dani Pedrisa [Honda], KTM's Pol Espargaro, Alex Rins [Suzuki], Aprilia's Aleix Espargaro and Ducati wildcard Michele Pirro.
Pirro, Aleix Espargaro and Rins all suffered late tumbles as well, but like Miller were unscathed from their offs.
The late flurry of laps saw Vinales shuffled back to 11th on the combined standings, meaning he will face Q1 along with teammate Rossi, while Suzuki's Andrea Iannone adds his name to the list of major scalps heading into the first part of qualifying.
Jorge Lorenzo continued to make steady progress as he gears up for his first race since crashing on the opening lap of the Aragon Grand Prix, and was 17th with a personal weekend-best of 1:41.026s. He too will go through Q1.
Avintia's Xavier Simeon was absent from FP3 and will sit out the remainder of his final MotoGP weekend, after suffering a suspected concussion following two crashes on Friday. Jordi Torres will be the sole representative for the team's home event.