Marc Marquez secured his 63rd career pole position with a new lap record at the Brno circuit.
Saturday morning's pace-setter Jorge Lorenzo was immediately up to speed as his opening gambit, a 1:54.959, smashed the pole record.
Marquez, despite admitting that the shoulder that he dislocated last weekend in Austria was not yet "100%", was second, 0.331s down with Hector Barbera third.
Heading out for a second run at the Brno circuit, Lorenzo upped his pace to a 1:54.849 to pull away from the chasing pack.
That, however, did not stop Marquez.
The championship leader stormed around Valentino Rossi and Pol Espargaro at the final chicane to post a new lap record of 1:54.596.
Lorenzo qualified second, 0.253s down, while Andrea Iannone put in a late burst to finish third. The Ducati rider was 0.631s off the pace.
Aleix Espargaro was fourth ahead of Barbera and Rossi.
Danilo Petrucci missed out on a Q2 berth as he was knocked down by Bradley Smith in the final minute of Q1.
Smith qualified P11 while Petrucci qualified 13th. He will, however, line up in 16th place as he has a three-place grid penalty for causing a collision at the previous race in Austria.
1 Marc MARQUEZ Repsol Honda Team 1'54.596
2 Jorge LORENZO Movistar Yamaha MotoGP 1'54.849 +0.253
3 Andrea IANNONE Ducati Team 1'55.227 0.631
4 Aleix ESPARGARO Team SUZUKI ECSTAR 1'55.324 0.728
5 Hector BARBERA Avintia Racing 1'55.437 0.841
6 Valentino ROSSI Movistar Yamaha MotoGP 1'55.509 0.913
7 Andrea DOVIZIOSO Ducati Team 1'55.748 1.152
8 Maverick VIÑALES Team SUZUKI ECSTAR 1'55.787 1.191
9 Dani PEDROSA Repsol Honda Team 1'55.841 1.245
10 Cal CRUTCHLOW LCR Honda 1'55.930 1.334
11 Bradley SMITH Monster Yamaha Tech 3 1'56.115 1.519
12 Pol ESPARGARO Monster Yamaha Tech 3 1'56.522 1.926
13 Danilo PETRUCCI OCTO Pramac Yakhnich 1'56.148
14 Scott REDDING OCTO Pramac Yakhnich 1'56.263
15 Eugene LAVERTY Pull & Bear Aspar Team 1'56.535
16 Stefan BRADL Aprilia Racing Team Gresini 1'56.718
17 Loris BAZ Avintia Racing 1'56.797
18 Yonny HERNANDEZ Pull & Bear Aspar Team 1'56.805
19 Alvaro BAUTISTA Aprilia Racing Team Gresini 1'57.062
20 Tito RABAT Estrella Galicia 0,0 Marc VDS 1'57.606