That mistake almost handed fourth place to top American Nicky Hayden, who crossed the line less than half a second from Dovizioso.
Another American, rookie Ben Spies, got an electric start and followed Pedrosa through from the second row to hold a threatening fourth place in the opening laps.
However, an unseen moment on lap three dropped the Monster Yamaha Tech 3 rider back to seventh.
Spies then worked his way forwards and took fifth from Hayden on lap 21 and was setting himself up for a move on Rossi (then in fourth) when he dropped back behind Hayden once again on lap 25.
Spies was visibly frustrated as he returned to the pits after finishing in sixth.
One place, but 20 seconds, behind Spies was team-mate Colin Edwards, with Marco Melandri (Gresini Honda), Mika Kallio (Pramac Ducati) and Loris Capirossi (Rizla Suzuki) completing the top ten.
Roger Lee Hayden, replacing the injured Randy de Puniet at LCR Honda, finished his first MotoGP race since Laguna Seca 2007 in eleventh place - as he and fellow stand-in Alex de Angelis (Interwetten Honda) fought to the flag to avoid being last.
Joining Pedrosa on the DNF list were Laguna Seca rookies Alvaro Bautista (Rizla Suzuki), Hector Barbara (Aspar Ducati), Marco Simoncelli (Gresini Honda) and Aleix Espargaro (Pramac Ducati). All fell except Barbera who looked to suffer a technical problem.
A two-weekend summer break will now take place under round ten of 18, at Brno in the Czech Republic, is held on August 13-15. Rossi is set to confirm his future plans at that event, which is immediately followed by the second and final day of in-season testing.
US Grand Prix:
5. N. Hayden
11. R. Hayden
12. de Angelis