Trailing 1-0 for most of the game, ex-Stanford Cardinal Jahn notched his first professional goal in the 83rd minute when he converted a cross from Sam Cronin for the equalizer.
His play of a San Jose corner kick in the 90th was knocked down by the arm of New York's Roy Miller, setting up a Wondolowski penalty try.
His first shot was stopped by New York goalkeeper Luis Robles, but Miller was called for being offside, thus awarding another kick to Wondolowski.
He found the mark for the game-winner on the second try.
San Jose (1-1-0) rebounded after dropping its opener to Real Salt Lake.
Eric Alexander scored for the Red Bulls (0-2-0).