The reigning 125cc champion dominated the session on his Repsol Suter, leading by nearly a second at one stage, before Aspar Suter's Julian Simon got Marquez's lead down to 0.684 seconds.
The result was Simon's best qualifying position since Estoril in May, but he ended the session with a high-speed crash at the crest on the exit of Turn 13. He escaped without serious injury.
Scott Redding continued his strong Misano form to put his Marc VDS Suter on the final front row spot.
Championship leader Stefan Bradl was edged down to sixth as others improved late on, before salvaging fourth place thanks to a last-lap push. With Marquez having won five of the last six races, Bradl's lead in the standings is down to 23 points.
Bradl will be joined on row two by two ex-MotoGP men in JIR's Alex de Angelis and Pons rider Aleix Espargaro.
Jules Cluzel tailed Marquez on what proved to be his pole lap and took seventh.
Both Espargaro brothers are in the top 10, with Pol starting eighth.
Redding's team-mate Mika Kallio had one of his stronger performances of a tough year and claimed ninth, followed by Speed Master's Andrea Iannone.