Wondolowski scored in the 19th, 72nd and 80th minutes to extend his league-leading goal total to 17 on the year.
Alan Gordon tapped home a loose rebound from 3 yards in the 63rd minute and Simon Dawkins scored at short range off a 79th-minute corner kick to complete the scoring for San Jose (12-4-4), which is four points clear of Real Salt Lake (11-7-3) in the standings.
San Jose is also four points ahead of Eastern Conference leader Sporting Kansas City in the Supporters' Shield chase.
San Jose scored four times after Real Salt Lake captain Kyle Beckerman was shown a straight red card in the 58th minute for delivering a retaliatory foul against Earthquakes midfielder Sam Cronin, who had just taken down RSL's Javier Morales with a sweep of his trailing leg.
The five-goal difference tied the Earthquakes' largest margin of victory, matching a 5-0 win against Dallas on April 22, 2000.
San Jose is unbeaten in its past 10 matches at Buck Shaw stadium, going back to last August.
Wondolowski's initial goal came from a diving back-post header to convert a cross-goal pass from Justin Morrow. His second was a near-post touch to slot home a cross from Shea Salinas, who beat Real Salt Lake left back Kenny Mansally - starting because of injuries on the club's back line - down the right wing.
Wondolowski completed the hat trick by pouncing on a through ball from Khari Stephenson.
Gordon was in the right place at the right time to benefit after Victor Bernardez's header from a San Jose free kick crashed off the back post, leaving Real Salt Lake goalkeeper Nick Rimando no chance to respond.
- San Jose Earthquakes
- Real Salt Lake
- San Jose
- Chris Wondolowski