The Padres won three of the four-game series and remain 2 1/2 games behind the first-place Dodgers in the National League-West. San Diego is 10-3 this season against the Giants, who fell 4 1/2 games out of first.
Bonds hit a two-run shot, his 26th home run of the season, in the fourth inning off Ismael Valdez.
Yankees star Alex Rodriguez and Boston catcher Jason Varitek were suspended for four games apiece and fined on Thursday, and six other players were punished for their roles in a bench-clearing brawl last week between New York and the Red Sox.
Yankees pitcher Tanyon Sturtze and Red Sox outfielders Gabe Kapler and Trot Nixon were suspended for three games and fined by Bob Watson, major league baseball's vice president of on-field operations. Yankees outfielder Kenny Lofton, Red Sox pitcher Curt Schilling and Red Sox designated hitter David Ortiz were fined.
Rodriguez, the Yankees' All-Star third baseman, and Sturtze are appealing their suspensions. Varitek, Kapler and Nixon also plan to appeal, Red Sox spokesman Glenn Geffner said.
"I thought it was too much, four games," Rodriguez said before Thursday's game against Baltimore. "I was surprised it was that harsh. I've seen some harsher actions over the last month and it's five games."
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