Fellow American Colin Edwards rode with a special stars and stripes livery on his Tech 3 Yamaha for his home race, but it did him no favours as he sunk from seventh to 14th, ahead of an equally disappointed Loris Capirossi on the third GSV-R.
Stoner's team-mate Marco Melandri finished what might be his final Ducati race in 16th, after running off track on lap ten - a mistake that relegated the Italian from ninth to 17th and last, a position that eventually went to Kawasaki's Anthony West.
Only one rider failed to finish and that was Rossi's team-mate Jorge Lorenzo.
The MotoGP rookie, who has been trying to rebuild his confidence after some nasty accidents, lasted less than half a lap at his first US Grand Prix before a brutal highside - which equalled his Shanghai accident in terms of height - sent the Estoril winner bouncing through the gravel and nursing a foot injury.
While Lorenzo spends the summer break healing his latest wounds, Rossi will have three weeks to savour a truly memorable victory before the Czech Republic Grand Prix at Brno on August 17.
US Grand Prix:
6. de Puniet
13. de Angelis