Dani Pedrosa took his third victory of the season at Motegi in Japan on Sunday, marking Spain's 400th grand prix win and the first ever at the circuit for a Repsol Honda MotoGP rider.
Fourth on the grid, Pedrosa spent the early stages of the race behind team-mates Casey Stoner and Andrea Dovizioso.
Stoner then ran wide on lap 5, with Dovizioso pulling in for a jump-start penalty shortly after, handing Pedrosa the lead.
The Spaniard, whose 2010 title hopes ended with a broken collarbone in last year's event, then pulled away from Yamaha's reigning world champion Jorge Lorenzo to claim a dominant 7.3sec victory.
"When you win it is always a great feeling, especially as in the last three races I had finished second," said Pedrosa.
"The race was very weird at the beginning with Stoner and Dovi really fast on the first few laps, they pulled away and then Casey had ran off and Andrea had a ride-through due to his jump start.
"I was alone in front with Lorenzo very close, but I tried to put my head down and push every lap to pull away. 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 at Honda's track is great."
Prior to Pedrosa's victory, the last win by a Honda rider at Motegi - a track built by Honda - was at the hands of Makoto Tamada on a satellite 990cc RC211V in 2004.
Pedrosa, who missed three races this year due to another collarbone injury, is now just one point behind third in the championship Dovizioso, who finished fifth.
Stoner recovered to third place and leads the championship by 40 points from Lorenzo, with three rounds to go.