Less than a second separated the top five on the fourth lap, with Crutchlow in sixth slipping back as he struggled to match the leading group's pace on the M1.
Bautista almost rammed Rossi at the opening turn at the beginning of the fifth lap, with the mistake costing the Gresini Honda rider valuable time and gifting Rossi an advantage of around a second in fourth.
It seemed a matter of time before Lorenzo was forced to relinquish his lead and by the sixth lap both Repsol Honda riders had made their move.
Pedrosa took over with a pass at the last corner at the end of lap five before Marquez slipped underneath Lorenzo on the brakes at Turn one.
The Yamaha title challenger showed his fighting spirit as hit back to move swiftly back into second with a clinical move at Turn three.
There was then contact between the duo when Lorenzo bumped Marquez on the exit of Turn 10 after the title favourite had gone underneath with a trademark pass on the brakes.
With Lorenzo and Marquez disputing second, Pedrosa was able to open a gap of over half-a-second as he began to pull away at the front.
Rossi was unable to make an impact in fourth, although Crutchlow was now closing in on Bautista and took fifth place on the eighth lap.
Marquez seized second from Lorenzo once and for all on lap nine as Pedrosa nursed an advantage of almost two seconds and quickly put daylight between himself and Lorenzo, but Pedrosa looked in control as he managed the gap to his 20-year-old team-mate.
Bautista and Crutchlow were locked in a personal battle for fifth place, with Smith holding a safe sixth, well clear of Ducati's Andrea Dovizioso.