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Riding a Ducati, Capirossi got off to a strong start at the 4.8km Motegi circuit and finished with a time of 43 minutes, 13.585 seconds over 24 laps in perfect conditions.
Reigning world champion Valentino Rossi was second in 43:18.673 and Australian Grand Prix winner Marco Melandri had a time of 43:21.963 to complete an Italians sweep of the podium.
American Nicky Hayden, who leads the overall MotoGP standings, finished fifth. With two races left, Hayden leads Rossi by just 12 points.
Earlier, local favorite Hiroshi Aoyama won the 250cc race, crossing the finish line ahead of Alex De Angelis of San Marino.
Aoyama, riding a KTM, clocked a time of 43 minutes, 36.310 seconds to finish 1.341 seconds ahead of De Angelis on an Aprilia.
Jorge Lorenzo of Spain finished third on an Aprilia with a time of 43:40.659.
With two races left, Lorenzo leads the overall championship standings with 265 points. Andrea Dovizioso, who was fourth in Sunday's race is second with 238 points.
In the 125cc race, Finland's Mika Kallio edged world champion Alvaro Bautista of Spain for his third title of the season.
Kallio, riding a KTM, completed 21 laps in 41 minutes, 40.970 seconds, 0.185 seconds ahead of Bautista on an Aprilia.
Spain's Julian Simon, also riding a KTM, was third with a time of 41:48.739.
Bautista clinched the 2006 world 125cc championship with a win at the Australian Grand Prix a week ago.