World Champion Valentino Rossi finished second to Capirossi but importantly gained more ground on championship leader Nicky Hayden, closing the Americans lead to just 12 points with two races left.
"It was an amazing race," Capirossi said after the race.
"I saw Valentino closing the gap so I knew I had to give another push to take me to safety. This is the best of the two wins I've had in Japan."
Fellow Italian Marco Melandri finished third behind Rossi's Yamaha to move into outright third in the championship while Hayden had to settle for fifth place on his Honda.
Melandri's effort also helped clinch the constructors' title for Honda.
Hayden currently has 236 points with Rossi on 224. Melandri improved to 209 and Capirossi 205 to keep alive their slim hopes of snatching the riders' championship.
|Second straight title for Capirossi |
The fast finishing Rossi would have shaved another point off Hayden's lead if Japan's Shinya Nakano had not skidded out in the closing stages and allowed the American to move up from sixth to fifth.
However he remained delighted with the result on a track he openly dislikes as he bids to win his sixth consecutive premier-class title.
"These 20 points are so important for the championship," Rossi said.
"They're even more important at this track. It's not my favourite but we did a great job from the beginning."
In the 250cc category Japan's Hiroshi Aoyama won on his KTM as Spain's Jorge Lorenzo stretched his lead in the championship to 27 points after coming third on his Aprilia.