The Italian, who qualified on pole in the dry, began to pull away from championship leader Gabor Talmacsi with eight of the 21 laps to go, eventually winning by a safe 2.985secs.
Talmacsi was briefly demoted to third by Mike di Meglio, before the Frenchman fell and handed the runner-up position back to the Hungarian.
di Meglio rejoined in fourth, behind Talmacsi's Aspar Aprilia team-mate and title rival Hector Faubel - who has now slipped nine points behind Talmacsi with three rounds to go.
Race results – Motegi:
1. Pasini (Aprilia)
2. Talmacsi (Aprilia) +2.985secs
3. Faubel (Aprilia) +22.405secs
4. di Meglio (Honda) +33.751secs
5. Olive (Aprilia) +37.351secs
6. Corsi (Aprilia) +39.062secs
7. Nieto (Aprilia) +44.488secs
8. Gadea (Aprilia) +48.901secs
9. Ranseder (Derbi) +50.672secs
10. Iannone (Aprilia) +56.674secs
13. Webb (Honda) +1min 14.579secs