The 38-year-old Wondolowski announced his retirement immediately after the match in an on-field postgame ceremony.
"This organization is going to do big things in the future," Wondolowski told the audience. "Thank you to the fans. I can't thank you guys enough."
Wondolowski was in the starting lineup for just the ninth time this season in 32 appearances.
Wondolowski extended his MLS goal record to 171 -- with 167 coming over the past 13 seasons for the Earthquakes. He had five this season for San Jose (10-13-11, 41 points), which finished 10th in the Western Conference.
Jader Obrian scored his ninth goal of the season for FC Dallas (7-15-12, 33 points), who placed 11th in the West.
The Earthquakes had a hefty 28-7 edge in shots and placed seven on target to FC Dallas' one. San Jose had a 10-0 edge in corner kicks.
Wondolowski tallied the game's first goal in the 34th.
Marcos Lopez possessed the ball just to the left of the net and he sent a pass back into the middle of the box. Wondolowski lined up the approaching ball and sent it into the left corner for the final goal of his stellar career.
In the 40th minute, FC Dallas had a chance to knot the score with a penalty kick but Ricardo Pepi's right-footed blast caromed off the crossbar.
Two minutes later, FC Dallas did score the equalizer. Jesus Ferreira delivered a long downfield pass that led to a breakaway attempt for Obrian, who kicked a right-footer past Vega.
San Jose out-shot FC Dallas 17-3 in the first half but placed just three on target. FC Dallas had one on target.
The Earthquakes came up empty on three stellar chances during an 18-minute stretch of the second half.
Cade Cowell took a right-footer from right in front of the goal in the 51st minute but Maurer made the kick save. Javier "Chofis" Lopez was wide left on a left-footed free kick in the 53rd minute and Paul Marie's right-footed free kick was stopped by Maurer in the 68th minute.