Marquez run ends as Pedrosa wins Czech MotoGP
Spain's Dani Pedrosa of Repsol Honda competes during the Czech Republic Moto GP on August 17, 2014 in Brno - by Joe Klamar
Pedrosa, who won at Brno in 2012, finished the 22 laps on the dry 5.4-kilometre (3.36-mile) circuit in 42min 47.800sec, ahead of Yamaha duo Jorge Lorenzo and Valentino Rossi, with Marquez finishing fourth.
Marquez was looking to become the first premier class rider ever to win the 11 opening races of a season.
Italian legend Giacomo Agostini won the opening 10 races of the premier class season in 1968, 1969 and 1970 at a time when he dominated the sport.
However, no one has ever won the first eleven -- in part because Agostini's perfect season in 1968 comprised only 10 events.
Marquez, who failed to make it to the podium for the first time since Australia last year, now tops the championship with 263 points, 77 ahead of Pedrosa and 90 ahead of Rossi.
As often this season, Marquez got off to a poor start from pole position, dropping to sixth place.
Lorenzo soon settled down at the front, followed by Pedrosa who overtook him on the fifth lap to nurse his lead with Lorenzo never really getting close enough to fight back.
Marquez clinched the third spot but instead of narrowing the gap on the two leaders, he found himself under heavy pressure from Rossi.
Shrugging off a heavy crash in Saturday's practice in which he injured the little finger on his left hand, Rossi, who has won five premier class races in Brno, breezed past Marquez midway through the race.
He finished more than five seconds ahead of the championship leader in what was the 190th time he finished on the podium in all classes of motorcycling Grand Prix.
Earlier on Sunday, Spanish Moto 2 championship leader Esteve Rabat dominated the race in his category ahead of Finnish teammate Mika Kallio and Germany's Sandro Cortese.
And in Moto3, Frenchman Alexis Masbou took his first career victory after beating Italy's Enea Bastianini and Britain's Danny Kent in a nerve-wracking finish that saw 16 riders cross the finish line within two seconds.