Biaggi Eases to Pacific Grand Prix Victory
Japanese rider Makoto Tamada crossed the line third, overtaking Sete Gibernau on the final lap in Motegi, but was later disqualified for bumping the Spaniard.
Biaggi came through a late wobble unscathed to win his second race of the season in 43 minutes, 57.590 seconds.
"Two laps from the end I nearly fell," said Biaggi, who started the race from pole position. "I really thought I was going down (when) the bike wobbled...it was a miracle I stayed on. I would like to dedicate this race to Daijiro Kato."
The Japanese rider died from injuries as a result of a horrific crash at the season-opening grand prix in Suzuka.
World champion Rossi preserved his lead in the overall standings with 282 points. Gibernau has 224 points and Biaggi 199 with three races to go.
Biaggi took the lead early in the 24-lap race and was never seriously troubled after a braking error sent compatriot Rossi into the gravel trap on lap seven.
The 24-year-old rejoined the track in ninth place, 8.6 seconds behind Biaggi.
But Rossi, champion in the final season of 500cc in 2001 and the inaugural season on MotoGP last year, steadily worked his way back up the field.
He overtook Hayden and Gibernau on the 19th lap to go second but he could not catch Biaggi.