The winning rally included an error on Mets reliever Vic Black. With pinch runner Cameron Maybin at third, Smith topped a ball to the first base side of the mound against Josh Edgin. The left-hander fell as he came off the mound to field the ball and was late with his throw to first as Maybin scored.
Despaigne gave up a double to David Murphy with two outs in the eighth, New York's first hit. David Wright followed with a game-tying single, knocking Despaigne out of the game.
The rookie right-hander was bidding for the first no-hitter in Padres history.