The close Lorenzo/Hayden battle was mirrored between Ben Spies and Andrea Dovizioso for fifth. Dovi looked to have finally grabbed the position from Spies into the last turn on the penultimate lap, but Spies out-braked the Italian into turn one.
Dovizioso's day then got a lot worse when he crashed out later on the final lap, joining only LCR's Randy de Puniet as failing to finish.
Reigning world champion Valentino Rossi, who qualified an equal-2010 worst of seventh, went wide at turn one and dropped as low as ninth later in the race. The Fiat Yamaha rider recovered to sixth, helped by Dovi's late exit, but was an enormous 27sec behind Stoner.
Rossi's friend Marco Simoncelli finished one-second behind him in seventh for San Carlo Honda Gresini, with fellow rookie Alvaro Bautista was eighth on the lone Suzuki GSV-R.
Simoncelli's team-mate Marco Melandri and Pramac Ducati's Aleix Espargaro completed the top ten.
Spies' Monster Yamaha Tech 3 team-mate Colin Edwards had a nightmare race, finishing lap one in 14th and only reaching twelfth at the flag.
Aragon was called up to replace the unfinished Balatonring circuit in Hungary. It is supposed to revert to reserve status after this year's event, but few will be surprised if Aragon remains on the MotoGP calendar for 2011 and beyond.
Aragon was the third of four MotoGP rounds in Spain this year. The final Spanish visit will be for the Valencia season finale.
Aragon Grand Prix: