Starting from pole position after dominating all three practice sessions, Stoner beat Yamaha’s world champion Lorenzo by 3.44 seconds at the Losail circuit in a dream debut with the works Repsol Honda team.
The Australian, who raced for Ducati last year, has now won 24 Grands Prix in the top category.
Spain’s Pedrosa, Stoner’s Honda team-mate, was struggling with a painful arm and looked exhausted after finishing just over five seconds behind the Australian, despite taking the lead on the opening lap and fighting an entertaining duel to the halfway point.
Valentino Rossi of Italy, winner of nine world titles across the classes but struggling with a shoulder injury, finished well off the pace in seventh in his first race with Ducati after leaving Yamaha.
