"This circuit has a lot of fast chicanes, changes of direction, and it can be hard work. But I did quite a lot of training during the summer break and I feel very confident the whole package is working quite well."
Nicky Hayden, the current world champion, recovered from a couple of disappointing practice sessions at the undulating, 5.4 km Masaryk Ring to snatch second place on his Honda in 1:57.164.
"Even though we haven't put in one quick lap in every session, quietly we've been reasonably close to the pace and perhaps a bit better than it looked on paper," said the American.
"This afternoon the warmer temperatures helped us."
Dani Pedrosa, Hayden's team mate, came third fastest with 1:57.179.
John Hopkins, Suzuki, who slid into the gravel near the end, completes the front row on Sunday.
Valentino Rossi, Yamaha, came sixth, one place ahead of Loris Capirossi of Team Ducati, last year's Czech MotoGP winner.
Stoner, who cruised to victory in the previous race in the US, tops the overall standings on 221 points, 44 ahead of seven-time world champion Rossi. Spaniard Pedrosa is third on 155.