Helped by a first turn accident for Karel Abraham - which also caught up fellow satellite Ducati rider Randy de Puniet - then a lowside crash for Andrea Dovizioso, Rossi was 14th and 7.4sec from Stoner by the end of lap one.
Rossi then rose to ninth by the middle stages, but faced a near seven-second gap to Barbera.
The seven time MotoGP champion instead found himself fending off rookie Cal Crutchlow (Tech 3) and Hiroshi Aoyama (Gresini) in the closing stages.
Crutchlow snatched the position from Rossi with an outside pass into turn one - completing a forgettable debut for the new 'aluminium' Ducati.
Joining Abraham and Dovizioso on the DNF list were Toni Elias (LCR) and Loris Capirossi (Pramac).
Capirossi tagged the rear wheel of Elias, sending them both down with seven laps to go. Elias proved he has lost none of his manners by checking on the slow-to-stand Capirossi as they walked away.
Like de Puniet, celebrating his 100th MotoGP star, Colin Edwards also had a miserable anniversary. The Texan began his 150th MotoGP race from 15th on the grid and was 13th and last at the flag.
The Repsol Honda team were riding in a special livery, created by Spanish designer David Delfi, today. Stoner's victory was the 100th for Repsol Honda in the premier-class.
MotoGP will now head for the first of three consecutive flyaway races, at Motegi (Japan) at the end of this month, before returning to Spain for the Valencia season finale.
Aragon Grand Prix:
12. de Puniet