The Earthquakes came into the game in contention for a playoff berth, but would have needed to score 13 goals and have Colorado lose Vancouver on Sunday.
Stephen Keel scored in the 90th minute for FC Dallas, which already had been eliminated from playoff contention.
David Bingham made his first start of the season for the Earthquakes.
San Jose's victory gave the retiring Ramiro Corrales a successful send off. The last original member of the MLS from 1996, Corrales made his first start since Sept. 14 and had two chances to score in the first 11 minutes.
The Earthquakes finished the season with a seven-match unbeaten streak and a 16-game unbeaten run at home.
Dallas, which ended its home season with a victory its last time out, went 1-5-1 over its last seven games.
Martinez came back from a missed shot in the 23th minute to give the Earthquakes a 1-0 edge four minutes later.
Wondolowski received a pass from Shea Salinas just inside the penalty box and fired a drive into the near top corner in the 57th minute.
San Jose went 11-5-3 under interim coach Mark Watson, who replaced Frank Yallop midway through the season. Watson remains a leading candidate to become coach.
Dallas coach Schellas Hyndman was on the sidelines for the final time after announcing earlier that he would retire following the season. He spent the past six years in the MLS.
Corrales leaves as the Earthquakes' leader in games played with 250. A brief, pregame ceremony was held for him and he received a standing ovation when he subbed out in the 60th minute and was carried off the field by teammates Steven Lenhart and Victory Bernandez.
Peter Luccin received a yellow card in the 85th minute.