After a very close morning battle was won by Yamaha's Jorge Lorenzo, the afternoon session was dominated by Honda.
Lorenzo and title rival Marquez immediately kicked off with their best laps of the day, but the latter's 1m48.987s was 0.418 seconds clear of Lorenzo's quickest effort.
This early-run times would stand as Marquez and Lorenzo's best of the day.
It was sufficient to keep Marquez on top for the rest of the session, but Lorenzo was pushed back to fourth.
First Marquez's works Honda team-mate Dani Pedrosa moved up to second, then LCR Honda rider Stefan Bradl put in a great lap to claim the spot, 0.132s slower than Marquez.
With Alvaro Bautista going fifth quickest for Gresini, Lorenzo was the sole Yamaha in a Honda-filled top five.
Bautista set his time on his first run and later had a crash at Turn 8. He was unhurt.
Yamaha riders Cal Crutchlow and Valentino Rossi were back in sixth and seventh, ahead of Ducati pacesetter Andrea Dovizioso and CRT leader Aleix Espargaro.