The Padres trailed by a run heading into the ninth, but got to New York closer Francisco Rodriguez and downed the Mets for the second straight game.
Rodriguez (2-3) walked Kyle Blanks to open the ninth, and Blanks scored the tying run on a double by Will Venable.
Venable went to third on the futile throw home, and Rodriguez then walked Henry Blanco and Oscar Salazar intentionally to load the bases in hopes of creating a force out at home.
Cabrera battled his way through a nine-pitch at-bat, falling behind 0-2 and eventually working the count full before hitting his homer to right.
Heath Bell (4-1) got the win by pitching the top of the ninth.