Stoner finished 22 laps of the 5.403-kilometer (3.358-mile) Brno circuit in 43 minutes, 16.796 seconds on a Honda to claim his sixth victory of the season.
Starting third on the grid, Stoner went ahead in the second lap after Spaniard Dani Pedrosa, who started from the pole, had a crash.
Stoner, chasing his second championship after 2007, dominated the rest of the race, steadily increasing his lead to seal a second straight win following his victory at Laguna Seca, California and his 29th overall in MotoGP.
Italian Andrea Dovizioso finished second, 6.532 seconds behind and another Italian Marco Simoncelli was third 7.792 back to complete a Honda clean sweep.
Stoner, who also won in Brno in 2007, tops the MotoGP standings with 218 points and leads defending champion Jorge Lorenzo of Spain by 32 points.
Lorenzo was fourth on his Yamaha, 8.513 behind Stoner, followed by Ben Spies of the United States on another Yamaha.
Dovizioso is third overall with 163 points and seven-time world champion Valentino Rossi, who finished sixth, is fourth on 118.
Andrea Iannone of Italy claimed the Moto2 on a Suter for his second season victory in 41:13.255, edging Spaniard Marc Marquez on another Suter by 0.161.
German Stefan Bradl on a Kalex finished third and remains top of the standings with a 43-point lead over Marquez.
Fellow German Sandro Cortese won the 125cc class on an Aprilia in 40:59.229 for his first career victory. French rider Johann Zarco finished second, 0.397 behind on a Derbi. Spain’s Nicolas Terol, who didn’t finish the race, retained the overall lead with 166 points. Zarco is second on 154.
