The Padres scored single runs in each of the eighth and ninth innings to erase a 3-2 deficit and rally for the win.
In the eighth, Yonder Alonso coaxed a leadoff walk from Gonzalez Germen, went to third on a one-out double by Chase Headley and came home with the equalizer when Chris Denorfia followed with a single.
After Huston Street (1-4) shut down the Mets in the top of the ninth, Venable led off the bottom of the inning against Pedro Feliciano (0-2) by golfing a 1-2 pitch just inside the right-field foul pole for the game-winner.
Nick Hundley went 3-for-3 with a run scored as San Diego earned a split in the four-game series.
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