Yamaha duo Jorge Lorenzo and Valentino Rossi finished second and third, with Marquez, who had hoped to become the first premier class rider to win the 11 opening races of a season, fourth.
Spanish world champion Marquez leads the 2014 standings with 263 points, 77 ahead of Pedrosa and 90 ahead of Rossi.
Marquez started from pole for the ninth time this season but he was beaten off the line by Andrea Iannone (Ducati) and Andrea Dovizioso (Ducati) before finishing the opening lap in sixth.
Lorenzo, who started from sixth position on the grid, surged through the field in the early stages and took the lead of the race.
But with 17 laps remaining Spaniard Pedrosa got the better of compatriot Lorenzo and passed the Yamaha rider before speeding to victory.
Marquez fought his way back up to third but he failed to keep pace with the two leaders and came under increasing pressure from Rossi.
With 10 laps remaining Marquez was unable to fend off Italian Rossi, who passed him and forced the 21-year-old off the podium for the first time this season.
(Reporting By Michael Hann, editing by Pritha Sarkar)
Share
