"I had a very good start and in first laps I thought maybe I could stay there two or three laps, then it became four or five," said a clearly shocked Pedrosa.
"As it went on I couldn't believe I was still there with the Yamahas."
Rossi was disappointed not to have won, but took consolation from scoring valuable championship points.
"I did a great start but after some laps I realised I didn't have enough pace to to away long," said Rossi.
Unexpected win in Japan delights Lorenzo
"After I got my rhythm, my pace was ok but too late to come back on Lorenzo - it's not a victory but it's 20 points for the championship."
Lorenzo admitted he did not expect to lead the championship so early in the season, and said he was looking forward to putting on a show in front of his home fans at the next round of the championship, in Jerez in Spain.
"Jerez is always a party, people are always pushing the Spanish riders so I think maybe well take some risks to try and win," he said.
"If we can't, we'll finish as best we can."
In the 125cc race, Italy's Andrea Iannone won his second consecutive race, ahead of Julian Simon and Pol Espargaro, to retain his lead in the championship.
Spain's Alvaro Bautista won the 250cc ahead of home favourite Hiroshi Aoyama, with Mattia Pasini in third.
Reigning champion Marco Simoncelli, who missed the opening race of the season because of a wrist injury, started from pole and led for the first nine laps until he clipped the kerb and struggled back to the pits, re-emerging to finish in 17th place.
MotoGP race result:
1 J Lorenzo (Spa) Fiat Yamaha 43 mins 47.238 secs 2 V Rossi (Ita) Fiat Yamaha 43:48.542 3 D Pedrosa (Spa) Repsol Honda 43:51.001 4 C Stoner (Aus) Ducati 43:52.929 5 A Dovizioso (It) Honda 43:56.445 6 M Melandri (Ita) Kawasaki 44:17.793 7 L Capirossi (Ita) Suzuki 44:19.994 8 M Kallio (Fin) Ducati 44:26.654 9 J Toseland (GB) Yamaha 44:30.344 10 C Vermeulen (Aus) Suzuki 44:30.483, 11 R de Puniet (Fra) Honda 44:32.072 12 C Edwards (USA) Yamaha 44:33.778 13 A de Angelis (Smr) Honda 44:40.763 14 N Canepa (Ita) Ducati 45:09.042 15 T Elias (Spa) Honda +1 lap
World Championship standings:
1 J Lorenzo (Spa) Fiat Yamaha 41 points 2 V Rossi (Ita) Fiat Yamaha 40 3 C Stoner (Aus) Ducati 38 4 A Dovizioso (Ita) Repsol Honda 22 5 D Pedrosa (Spa) Repsol Honda 21 6 C Edwards (USA) Monster Yamaha Tech 3 17 7 M Kallio (Fin) Pramac Racing 16 8 C Vermeulen (Aus) Rizla Suzuki MotoGP 15 9 A de Angelis (SM) San Carlo Honda Gresini 13 10 M Melandri (Ita) Hayate Racing Team 12
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