Stoner inherited third on the opening lap when Marco Simoncelli saw his best ever MotoGP
qualifying position, of second, wasted after a huge highside. Simoncelli (third) and Stoner (fourth) had previously survived a scare on the exit of turn one.
Simoncelli's highside - which was followed moments later by an accident at the same corner for Hector Barbera - blew the lead group apart.
Valentino Rossi made use of the incidents to carve his way up to fourth on lap 1, from ninth on the grid, then spent most of the race trying to hold off the third Repsol bike of Andrea Dovizioso.
Rossi succeeded until the final few metres of the race, when fellow Italian Dovizioso snatched the place from him by just 0.025sec. Fifth is Rossi's best dry result as a Ducati rider and matches his wet finish - after a crash - at Jerez.
Monster Yamaha Tech 3's Colin Edwards
held sixth place for almost the entire race, with Simoncelli's San Carlo Honda Gresini team-mate Hiroshi Aoyama taking seventh place after a long battle with Edwards' rookie team-mate Cal Crutchlow.
Joining Simoncelli and Barbera on the DNF list were Lorenzo's team-mate Ben Spies and rookie Karel Abraham.
Spies dropped from fifth to tenth after a mistake on lap two, and later tagged the rear of fellow American Nicky Hayden
as he made his way back up the order.
The Texan's progression came to an end when he crashed out of eighth place on lap 12, his second DNF from the three rounds this year.
Ducati riders Hayden and Randy de Puniet
were ninth and tenth at the flag, with LCR Honda's Toni Elias
eleventh. Loris Capirossi
took twelfth on the second Pramac bike.
Rizla Suzuki's Alvaro Bautista - returning to action after breaking his left femur during practice for round one in Qatar on March 18 - rode an understandably conservative race to 13th and last.
Estoril became round three of the 2011 world championship after the postponement of the Japanese Grand Prix.
A one-day test takes place at the track on Monday.
Portuguese Grand Prix:
10. de Puniet