Team-mate Valentino Rossi's race came to an abrupt end when he fell from a lonely eighth on entry to the corkscrew with three laps to go. The Italian's GP somersaulted into the airfence while he trudged away unharmed. Hayden gave Rossi a lift back to the pits after the race.
Alvaro Bautista finished a US GP at his third attempt, claiming eighth for Honda Gresini, while Aleix Espargaro won the CRT battle with ninth place for Aspar.
Cardion AB Ducati's Karel Abraham finished tenth on his return to action, with the remaining four finishers - Randy de Puniet
(Aspar), Yonny Hernandez (Avintia), Colin Edwards
(Forward) and Ivan Silva (Avintia) were a lap down.
Michele Pirro fell at the Hairpin on the opening lap, with Pramac Ducati stand-in Toni Elias
crashing out soon after. Mattia Pasini (Speed Master) and Danilo Petrucci (Ioda) retired, with James Ellison
(PBM) joining Spies and Rossi in hitting the deck.
Wild-card CRT rider Steve Rapp (Attack Performance) was unable to start the race after being unable to lap within the 107% qualifying time.
MotoGP will now have its summer break, which will end with the second US round at Indianapolis from August 17-19 - by which time Rossi's 2013 plans could well be known.
From the ten of 18 rounds so far held, Lorenzo has claimed five victories, Stoner four and Pedrosa one.
US Grand Prix:
1. Casey Stoner
2. Jorge Lorenzo
3. Dani Pedrosa
4. Andrea Dovizioso
5. Cal Crutchlow
6. Nicky Hayden
7. Stefan Bradl
8. Alvaro Bautista
9. Aleix Espargaro
10. Karel Abraham
11. Randy De Puniet
12. Yonny Hernandez
13. Colin Edwards
14. Ivan Silva