Lorenzo was dropping off the pace as his challenge faded, although Marquez was unable to make any significant headway on Pedrosa and appeared to settle for second place and a haul of 20 points.
The action was taking place behind the top four as Crutchlow and Bautista fought it out for fifth, with Bautista keeping a tight line at the hairpin on the final lap to deny the British rider.
Pedrosa celebrated his first win since Jerez at round three, taking the chequered flag with 2.757s in hand over Marquez, with Lorenzo almost a further four seconds in arrears.
Rossi - who carried a Marco Simoncelli tribute flag on his slowing down lap - bagged a solid fourth followed by Bautista and Crutchlow, with Smith seventh ahead of Dovizioso and Aleix Espargaro on the Power Electronics Aspar.
Yonny Hernandez rounded out the top ten on the Ignite Pramac Ducati.
American Nicky Hayden was forced out of the race with smoke emanating from his Desmosedici, while Andrea Iannone (Pramac Ducati) and Damian Cudlin on the PBM machine also failed to finish.
There was more bad luck for Paul Bird's team when Laverty went down at the hairpin as both PBM riders failed to finish for the second consecutive time.