With track-side temperatures passing 45 degrees Celsius (113 Fahrenheit) the riders burned up the circuit.
With the clock ticking Andrea Iannone, on a Suzuki, held provisional pole but after all the riders out on the course had finished, the Italian was relegated to 10th.
Championship leader Marquez was quickest in 1 minute 32.791 seconds. The Honda star finished 0.041 seconds faster than team-mate Cal Crutchlow. Italian Valentino Rossi (Yamaha) completed the front row another 0.018 seconds back.
The first four riders were separated by less than one tenth of a second and the top 11 by just half a second. “It was difficult,” Marquez said, adding that “I felt I had a good rhythm even if this is not my strongest circuit.”
“But I’m starting from pole position tomorrow.”
“Nice to have a front row,” said Crutchlow, who is sixth in the championship standings.
He said adding that he felt he had lacked speed in the final section of the course but added that, “the whole Honda family is doing a good job.”
Rossi, who has won 10 races, including eight grand prix at Assen completes the front row. “I am very happy,” the Italian said.
“Especially after I went off the track in the second practice session, but I managed to find the right set-up to be able record a great time and start from the front row.”