Pedrosa had a violent high-side just after a close moment with Honda team-mate Marquez on lap six of the MotoGP race, as they battled for second behind Yamaha's Jorge Lorenzo.
Marquez ran wide in an attempt to go down the outside of Pedrosa, but while he skated over the run-off area, Pedrosa crashed on acceleration out of the corner.
Honda is investigating whether an earlier brush between its two bikes damaged Pedrosa's traction control system, causing his accident.
Marquez felt that they both had separate incidents.
"I went wide and then I saw that he crashed," he said.
Pedrosa was taken to the medical centre for checks on a potential left knee injury, but was found to have escaped any serious harm.
Marquez went on to catch Lorenzo and beat him to victory.
The result means Marquez leads the championship by 39 points over Lorenzo with four races left, with Pedrosa a further 20 adrift.