The Spaniard, who has come back well after missing three races earlier this season with a collarbone injury, benefited from an error by team-mate Casey Stoner to come through for his third win of 2011.
Pedrosa led home the Yamaha of reigning champion Jorge Lorenzo, while Stoner recovered from an trip across a gravel trap to take third place.
Twelve months ago Pedrosa suffered agonies at the Motegi circuit when he picked up shoulder and ankle injuries in a practice crash, but a year on he was in a league of his own after Stoner's error, taking victory by over seven seconds.
"I was alone in front with Lorenzo very close, but I tried to put my head down and push every lap to pull away," said Pedrosa.
"I'm really happy because at this track I've had a mix of good and bad results and some bad injuries, so come back one year later and win in MotoGP is fantastic."
The outcome sees Stoner's lead in the MotoGP riders' standings cut to 40 points by Lorenzo with three rounds remaining. With 195 points, Pedrosa trails Stoner by 105 and was already out of the title race, but now just sits one point behind fellow Honda rider Andrea Dovizioso in the scrap for third.
Stoner made a clean start from pole position to lead into the first corner but there was drama moments later when Ducati's Valentino Rossi and Yamaha's Ben Spies got together in turn three.
Spies was able to recover his bike and continue but Rossi's race was run as the Italian registered his first retirement of his disappointing debut campaign with Ducati.
The pack was shuffled still further when Dovizioso, Cal Crutchlow (Tech 3 Yamaha) and Marco Simoncelli (Gresini Honda) were all handed drive-through penalties for jump starts. That was good news for Stoner, who after his off on lap five had dropped to seventh but was soon up to fifth when Dovizioso and Simoncelli peeled off.
Fifth became fourth when the Australian passed Ducati's Nicky Hayden, before dispatching Suzuki's Alvaro Bautista to salvage third.
"It's really disappointing as we had the bike to win here today," said Stoner.
"But in the end I guess I should be thankful that we were able to climb back up to a podium spot after other peoples misfortunes and mistakes on track."
Bautista's strong race ended in tears when he lost control with seven laps remaining and crashed in turn 12. The Spaniard's exit meant Simoncelli took fourth ahead of Dovizioso, while Spies was sixth.
The staging of this weekend's race had been in doubt after it was moved from its original April date due to Tohoku earthquake and tsunami and the resulting nuclear accidents at the Fukushima power plant.
Several riders had pondered boycotting the race due to fears for their health due to radiation levels in Motegi, which is just over 120 kilometres from Fukushima, but in the event a full complement of riders was in attendance.