The England international scored one goal and set up another in the win.
Beckham ran on to a pass from Landon Donovan in the eighth minute and sent a low right-foot shot past goalkeeper Joe Cannon for the opening goal at the Home Depot Center.
The former Manchester United and Real Madrid player was on target in a SuperLiga clash against DC United last season but his goal against San Jose was his first in league play.
Beckham's lofted ball over the San Jose defence after 36 minutes set up United States international Donovan, who lobbed the advancing Cannon from the edge of the penalty area.
"It's always nice to get a goal and it was great to help the team get the win," Beckham told reporters. "It was a good team performance and it was important to bounce back from the weekend."