The visitors took the lead after just two minutes at Dick's Sporting Goods Park through Marvin Chavez.
Wondolowski made it 2-0 to San Jose nine minutes later when he turned home Rafael Baca's cross.
The 29-year-old was on target again in the 51st minute when his shot from the edge of the Colorado penalty box deflected off Drew Moor into the home side's goal.
Wondolowski completed his hat-trick and scored his 25th goal of the season seven minutes from time, slotting home Sam Cronin's pass with ease.
Colorado pulled one back for a consolation goal in injury time through Andre Akpan.
Jason Hernandez pulled down Akpan inside the area and was promptly dismissed, with the 24-year-old making no mistake from the spot.