Wondolowski almost had the hat trick, but he hit the goal post from close range in the 87th minute.
Toronto (0-2) has never beaten San Jose at home, going 0-2-3.
Toronto showed flashes of style on offense, but did not have the clinical finish to take advantage. And it was let down by its defense.
Manager Aron Winter's team has allowed six goals in two MLS games this season. Toronto lost its season opener 3-1 in Seattle and left the field Saturday to a few boos.
''Two games, six goals,'' Winter said.
The opening goal came nine minutes in when former Toronto FC midfielder Sam Cronin found Wondolowski unmarked in the penalty box. The San Jose forward, whose six-game scoring streak was snapped last week against Houston, headed it past Milos Kocic.
The goal followed a corner after Kocic parried a Salinas strike. San Jose (2-1) pressed from the beginning.
''I hate conceding goals and this is a terrible start to the season for me,'' Kocic said. ''Six goals in two games. It's not how defenders should play, including all of us.''
Toronto began to put some passes together and Ryan Johnson had a chance in the 27th, but couldn't get a clean shot at the ball as a defender harassed him in the box.
The Earthquakes went on the counter-attack in the 56th minute as Salinas slotted a low shot past Kocic.
San Jose made it 3-0 in the 67th minute. Rafael Baca broke in on the right and sent the ball across the box as Kocic rushed out. Wondolowski had plenty of time to get control of the ball and score.
''We were not happy in the locker-room after the game ... It was not a good game from our side,'' Winter said. ''There are a lot of things we didn't do well today.''
The game was the first of five in 14 days for Toronto, which is combining MLS play with the CONCACAF Champions League. Next up in that competition is Mexico's Santos Laguna, which visits BMO Field on Wednesday to open the two-leg semifinal.
- Toronto FC
- San Jose Earthquakes
- Shea Salinas
- Chris Wondolowski
- San Jose