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 winner of the Nov. 1 match between Los Angeles Galaxy and 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.
COMMERCE CITY, Colo. -- The Colorado Rapids found little satisfaction with a two-game winning streak.
"We played hard and we played well," Colorado forward Andre Akpan said. "We won our last two games, but we aren't going to the playoffs."
Akpan and Kamani Hill scored to help the Rapids beat the playoff-bound Houston Dynamo.
Colorado (11-19-4) finished one of the worst campaigns in franchise history with only its second two-game winning streak of the year. The Rapids were 3-5-3 in their last 11 games.
Goalkeeper Steward Ceus needed to make only two saves as he posted his second shutout in his second career MLS start.
"I saw a lot of spirit and a lot more confidence the last two games and that was expressed in the field," Rapids coach Oscar Pareja said. "The team played the way wanted, but it came at the end of the year."
Houston (14-9-11) had already rapped up fifth place in the Eastern Conference and its sixth playoff appearance in seven years. The Dynamo will play Chicago in the wild-card game Wednesday night in Chicago.
Houston rested many of its regulars including its top five goal scorers and starting goalkeeper Tally Hall. Tyler Deric subbed for Hall and made his first career MLS start.
CHESTER, Pa. -- Kenny Cooper scored twice, and Thierry Henry added a goal to lift the New York Red Bulls.
The Red Bulls (16-9-9) reached the playoffs for the third straight year, and the ninth time in 10 seasons. New York won all three matches this season against the Union (10-18-6), who lost their final three games and will miss the postseason for the second time in three years.
Cooper scored on a penalty kick in the 13th minute after Tim Cahill was taken down by defender Carlos Valdes in the box a minute earlier. Henry scored his 15th goal to make it 2-0 in the 35th minute.
Cooper added his team-leading 18th goal -- and fifth against Philadelphia this season -- in the 66th minute.
The Union played without defender Sheanon Williams (left ankle), defender Gabriel Farfan (right ankle) and midfielder Freddy Adu (coach's decision)
BRIDGEVIEW, Ill. -- Lionard Pajoy scored in the 50th minute, and Bill Hamid made eight saves to help D.C. United rally.
The draw gave D.C. second place in the Eastern Conference.
United (17-10-7) went 5-0-2 in its last seven matches to finish with 58 points, one more than New York and Chicago (17-11-6). New York finished third, ahead of fourth-place Chicago, on a tiebreaker.
With New York beating Philadelphia earlier in the day, the Fire needed to beat D.C. to avoid playing in the first-round one-game elimination round.
Instead, Chicago will host fifth-place Houston in that game. It will be played either Wednesday or Thursday. The winner plays Eastern Conference champion Kansas City in the second round.
Pajoy beat Sean Johnson with a diving header in the 50th minute.
Pajoy's eighth goal of the season, and third since joining United from Philadelphia, was one of D.C.'s few good chances. United was held to two shots on goal in the first half and five for the game, including a carom by Pajoy in the 70th minute that Johnson cleared off the line.
Chicago took nine shots on goal, but only forward Patrick Nyarko beat Hamid. He right-footed a 24-yard shot low to Hamid's left side in the 16th minute for his fourth goal of the year.
Every opportunity after that, the Fire either misfired or squandered. In the last 25 minutes, Dominic Oduro, Serjill MacDonald and Jalil Anibama all had close-in opportunities that were either saved by Hamid, hit the post, flew over the crossbar, or, in the case of Oduro's last shot, were blocked by midfielder Nick DeLeon. Hamid's eight saves matched his season high.
MONTREAL -- A.J. Soares scored in the 89th minute to lift the New England Revolution.
Soares was inside the box to head Chris Tierney's free kick past the reach of goalkeeper Troy Perkins for an unsatisfying end to a game the Impact mostly dominated.
The Revolution (9-17-8) ended a 13-game winless run in road matches and won for the first time on Canadian soil, having previously gone 0-5-3 in Montreal, Toronto and Vancouver.
The Impact (12-16-6) ended the campaign with a loss like many they sustained this season -- on a late goal off a set piece.
SANDY, Utah -- Real Salt Lake played to a draw with the Vancouver Whitecaps and made a little bit of history along the way.
RSL (17-11-6) became just the second MLS team to not allow a goal in the first 15 minutes of any regular-season match when it held Vancouver (11-13-10) scoreless before halftime. Houston also accomplished the feat in 2009.
Both offenses were listless for much of the half, but stepped up the attack in the closing minutes before halftime. Vancouver had a golden chance to strike first when Alain Rochat put a left-footer perfectly on frame in the 37th minute. RSL keeper Kyle Reynish made a leaping save to deny the goal.
RSL had a near miss of its own in the 38th minute. Alvaro Saborio curled in a left-footer from the left side of the box. Whitecaps keeper Brad Knighton barely tipped the shot away to prevent a goal and set up a well-defended corner kick.
Vancouver blew another chance to take a lead in the 57th minute. Rochat played a through ball perfectly to Darren Mattocks by the left post. Mattocks tapped it in for an apparent goal, but it was waved off because Mattocks was ruled offside.
Salt Lake's best chances came in the 69th minute when Luis Gil could not sneak a right-footer from distance past Knighton and in the 72nd minute when Steele was denied by Knighton after trying to put it in from the center of the box.
Both teams qualified for the playoffs.