The historic strike came from the penalty spot in the 76th minute of San Jose's 3-1 win over Minnesota United, with the Earthquakes having gone in front just two minutes in from a Magnus Eriksson penalty.
Christian Ramirez pulled Minnesota back level in the 27th, but a Wondolowski assist to Danny Hoesen in the 70th put San Jose back in front.
Francisco Calvo handled the ball in the area leading to the bit of history for Wondolowski, who confidently slid the ball into the corner to break the record.
While it was strike 132 for the Earthquakes, the goal was the 35-year-old's 136th career MLS goal, leaving him just nine short of Landon Donovan's all-time record
The win was just San Jose's second of the year, moving the club off the bottom of the Western Conference table for the moment, though the Earthquakes are level on points with the Seattle Sounders, who play against the Portland Timbers on Sunday.
For Wondolowski, the goal was his second of the campaign, and his 23rd from the penalty spot across the course of his career.
In 2017 Wondolowski scored 13 times and will need to come within one goal of that mark to take the outright lead on Donovan as the league's all-time leading scorer.
San Jose Earthquakes (@SJEarthquakes) May 12, 2018
San Jose will be back in action Wednesday against the Vancouver Whitecaps.