Dani Pedrosa won the San Marino MotoGP for Honda, beating the Yamahas of fellow Spaniard Jorge Lorenzo and Italian Valentino Rossi.
But the race was overshadowed by the death of Japanese rider Shoya Tomizawa in the preceding Moto2 event.
The race continued and was eventually won by Spain's Toni Elias.
Pedrosa's victory keeps the pressure on Lorenzo - who had a 68-point lead going into this race - for the overall title with six races left in the season.
Stoner was falling down the field at an alarming rate as he was then passed easily by Italian Andrea Dovizioso.
Spanish rider Dani Pedrosa (Honda) won the San Marino MotoGP at Misano on Sunday to record two successive victories in the category for the first time.
The 24-year-old Pedrosa started from pole and never relinquished his grip on the race and came home for his fourth victory of the series ahead of championship leader and compatriot Jorge Lorenzo on a Yamaha. Italy's multiple champion Valentino Rossi, also on a Yamaha, was third.
Pedrosa's victory keeps the pressure on Lorenzo - who had a 68-point lead going into this race - for the championship title with six races left in the season.
Dani Pedrosa won the San Marino Grand Prix from the pole Sunday in a race overshadowed by the death of a rider in the Moto2 event.
Lorenzo stays top of the standings with 271 points, 63 ahead of Pedr