The Italian's Yamaha team-mate Jorge Lorenzo is thought to have broken a bone in his foot after coming off in spectacular fashion early in the race.
The battle for the lead between Rossi and Stoner was the closest and most exciting there has been this season, but afterwards Stoner was clearly not entirely happy with the way it had been fought.
"I completely made the mistake, it was all my own (going off the track)", he told BBC Sport.
"But at the beginning of the race, with some of those overtaking moves, I was so nearly on the floor that it wasn't funny.
"I know it's hard racing, I've been in hard racing all my life, but some of that was past the point. I don't think it was necessary."
But Rossi was adamant he had done nothing wrong.
"This is racing, every overtake was very clear for me - I never touched him," he said.
"The reality is I am stronger in braking, so I try to use this advantage. I deserved it, I think he made the mistake alone - it happens."
Rossi now goes into the summer break with an entire race-worth of points advantage on Stoner, who is second in the championship standings, and Dani Pedrosa's failure to compete this weekend has all but ended his slim title hopes.
"It was a great weekend," said Rossi.
"These 25 points are like gold for our championship."
Briton James Toseland finished ninth, having been in seventh for much of the race, but he said he was glad to have improved on his recent poor run of form.
Toseland was frustrated by his tyres' performance
"I tried to keep those guys behind but I'd pretty much shot the rear tyre by the end," he told BBC Sport.
"The team's working well but we've had some problems behind the scenes which need to change for the next race.
"I've been riding round, not racing round, and I don't like that. To be in the top 10 is nice but the potential is there to be a lot better."
The next round of the MotoGP championship is at Brno in the Czech Republic on 17 August.
US MotoGP result:
1 V Rossi (Italy) Yamaha 44mins 04.311secs 2 C Stoner (Aus) Ducati 44:17.312 3 C Vermeulen (Aus) Suzuki 44:30.920 4 A Dovizioso (Ita) Honda 44:39.212 5 N Hayden (U.S.) Honda 44:39.974 6 R de Puniet (France) Honda 44:41.979 7 T Elias (Spain) Ducati 44:45.940 8 B Spies (U.S.) Suzuki 44:46.238 9 J Toseland (GB) Yamaha 44:47.330 10 S Nakano (Jpn) Honda 44:48.702
World championship standings:
1 V Rossi (Ita) Yamaha 212 2 C Stoner (Aus) Ducati 187 3 D Pedrosa (Spin) Honda 171 4 J Lorenzo (Spn) Yamaha 114 5 A Dovizioso (Ita) Honda 103 6 C Edwards (US) Yamaha 100 7 C Vermeulen (Aus) Suzuki 89 8 N Hayden (US) Honda 84 9 J Toseland (GB) Yamaha 72 10 S Nakano (Jpn) Honda 70
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