Wondolowski has three goals this season for San Jose (0-2-2).
Federico Higuain scored his fourth goal of the season with left-footed strike in the 44th minute for Columbus (3-1-1). The Crew are unbeaten in three road games this year.
Columbus created the best buildups in a first half marked mostly by end-to-end counterattacks. Higuain finally cashed in one of those chances just before the half, slipping in unmarked while Hector Jimenez found Waylon Francis with a diagonal pass. Francis took the ball to the end line before turning in a grounded cross for Higuain to slot home with his left foot from 12 yards.
San Jose nearly tied it in the 47th minute when Yannick Djalo, freshly inserted at the half, took a short corner and beat Steve Clark with a delicate chip that ricocheted off the back post and out
The Quakes continued their pressure and tied on their fifth corner kick in the opening 6 minutes of the second half. Wondolowski got in behind Victor Bernardez's near-post run and headed home Shea Salinas' delivery.
Crew forward Dominic Oduro beat Earthquakes goalkeeper Jon Busch with a strong header in the 82nd minute, but crashed off the crossbar. Wondolowski came close in the 89th minute after being freed by a lead pass from Jean-Baptiste Pierazzi, but his shot tailed wide of the near post.