Spain's Jorge Lorenzo secured his fourth pole of the season, ahead of Briton Cal Crutchlow, for the Czech MotoGP at Brno.
The championship leader finished 0.196 seconds ahead of Crutchlow, who enjoyed his best-ever qualifying after signing a new Yamaha Tech 3 deal.
Dani Pedrosa, who is 18 points behind Lorenzo in the standings, qualified third with American Ben Spies fourth.
Casey Stoner will miss the race after breaking his ankle at Indianapolis.
The 26-year-old Australian, who retires at the end of the season, says he has "no idea" when he will return but admits his hopes of defending his title are over.
Stoner lies in third place in the standings, 39 points behind Lorenzo with seven races remaining.
Lorenzo, who won in Brno in 2010, set a new lap record despite admitting his team had struggled with their set-up all week.
"We started in a very good way in the first practice but then we couldn't improve the bike, we tried everything and it was impossible," said Lorenzo.
"So we came back to last year's setting here, the first time I tried the 1,000 (cc), and from the beginning I felt much better.
"I just enjoyed riding and improving the lap time. A very good feeling again, a very good pace and I think we are ready."
Crutchlow crashed halfway through the session and had to use his second bike, while Spain's Pedrosa, who also crashed early on, was 0.528 seconds behind after dominating all three free practices.
"It's nice to be back in the top three," said Crutchlow. "Hopefully we'll make it in the race. I don't think we're far away. I like the track here and it suits my riding style.
"It's a great track, so smooth. I managed to find the only bump. My own fault."
Italians Andrea Dovizioso (Yamaha) and Ducati star Valentino Rossi qualified fifth and sixth.
Qualifying times for Czech MotoGP:
1. Jorge Lorenzo (Spa) Yamaha 1:55.799
2. Cal Crutchlow (GB) Yamaha 1:55.995
3. Dani Pedrosa (Spa) Honda 1:56.327
4. Ben Spies (US) Yamaha 1:56.331
5. Andrea Dovizioso (Ita) Yamaha 1:56.559
6. Valentino Rossi (Ita) Ducati 1:56.735
7. Stefan Bradl (Ger) Honda 1:56.827
8. Alvaro Bautista (Spa) Honda 1:57.068
9. Karel Abraham (Cze) Ducati 1:57.773
10. Randy de Puniet (Fra) Aprilia 1:57.844