Heavy overnight rain meant it was only in the final few minutes that slicks could be used, and not all the frontrunners felt it was worth trying them.
Marquez put his Honda on top by over a second for a while as he led progress towards competitive dry times, although his final 1m54.797s was still seven seconds down on last year's pole.
He ran off the track after setting that time, keeping his Honda upright through the gravel only to then fall when he tried to cross the wet grass back onto the track.
The Spaniard was unhurt and managed to bump-start his bike and rejoin.
The order was predictably unusual as timing of slick laps decided the standings.
Ducati test rider Michele Pirro took second, followed by LCR Honda's Stefan Bradl and CRT duo Karel Abraham (Cardion) and Yonny Hernandez (Paul Bird). The latter was fastest overall for a spell.
Championship leader Dani Pedrosa set the best wet-tyre time of the morning, but ended up eighth.
The Yamahas did not try slicks, leaving Jorge Lorenzo and Valentino Rossi 14th and 16th.
Andrea Dovizioso crashed his Ducati at the first turn without drama. Ioda team-mate Lukas Pesek and Danilo Petrucci were the others to fall.