Wondolowski scored in the 24th minute, matching the record set by Roy Lassiter of Tampa Bay in 1996. The 29-year-old forward booted a penalty kick into the lower left corner of the net after Portland goalkeeper Donovan Ricketts was whistled for taking out Steven Lenhart in a race to secure the ball.
San Jose (19-6-9) has already secured its second Supporters' Shield and home-field advantage throughout the playoffs. The Earthquakes went undefeated in their last 10 matches and lead the league with 72 goals. They will face the Los Angeles Galaxy or Vancouver Whitecaps in first round.
The Timbers (8-16-10) appeared to be going down to defeat in the cold, steady drizzle until Bright Dike scored his fifth goal in the 67th minute to tie the score and put some life into the Portland attack.
Dike's goal came as he followed his own errant shot, which had been deflected by San Jose keeper Jon Busch. The pace of the game quickened significantly as both teams pushed on offense, but neither team could manage a clear shot. San Jose outshot Portland 10-8 for the game.
The Timbers have struggled through a disappointing season that saw coach John Spencer fired and replaced on an interim basis by general manager Gavin Wilkinson. The Timbers have spent the much of the time since Spencer was fired in July retooling the lineup and preparing for Akron coach Caleb Porter to take over as coach in 2013.
However, Portland did beat Vancouver 1-0 last week to take the Cascadia Cup series between the Timbers, Whitecaps and Seattle. Portland sold out boisterous Jeld-Wen Field for the 34th consecutive game Saturday.