Shoya Tomizawa, winner of round one and on pole for round two, returned to the head of the Moto2 field during qualifying for round nine in the Czech Republic.
The Technomag-CIP rider finished the session 0.232sec ahead of Fimmco Speed Up's Andrea Iannone, winner of two races this season.
Title leader Toni Elias, who was banned from Friday practice as punishment for a test session at Misano last Sunday, had been fastest in Saturday morning practice and will start the race from third on the grid for Gresini Moriwaki.
Roberto Rolfo completed the front row for the Italtrans STR (Suter) team, with Tech 3's Yuki Takahashi heading row two.
Second in the championship Thomas Luthi, 42 points behind Elias, will start just 13th for Interwetten Moriwaki.
Local star Karel Abraham, second on Friday, crashed heavily early in the session, forcing some frantic repairs by the Technomag-CIP team to get the Czech (due to be confirmed as a satellite Ducati MotoGP rider this weekend) back out on a track his father co-owns.
Abraham duly returned... then had an even bigger crash with 13 minutes to go, that left his bike upside-down against a tyre wall. Abraham trudged away and will start the race from 34th position.
Qualifying - Brno:
1. Tomizawa (Suter) 2m 3.452s
2. Iannone (Speed Up) +0.232s
3. Elias (Moriwaki) +0.289s
4. Rolfo (Suter) +0.342s
5. Takahashi (Tech 3) +0.693s
6. Aegerter (Suter) +0.799s
7. Corsi (Motobi) +0.931s
8. Tode (Suter) +1.032s
9. Simon (Suter) +1.067s
10. Redding (Suter) +1.076s