The Repsol Honda rider, fastest for most of the opening day of 2008 track action, sustained the injury after losing the front of his factory machine on the entry to turn 11 of the Malaysian Grand Prix circuit.
His bike then burst into flames after the fuel tank was ruptured, leaving little left undamaged by the time it was returned to the pits.
Pedrosa, who fortunately avoided the flames, was taken to a nearby hospital where scans confirmed a fracture and he has now returned to Spain for surgery, which is expected to take place this (Wednesday) afternoon.
Recovery time is still unknown, but he is certain to miss next week's Phillip Island test, meaning a loss of at least five days' track time.
Dani, the only Honda rider to win last season, had earlier escaped injury in a smaller morning fall.
