Xavier Nady began the comeback earlier in the ninth with a pinch-hit solo homer against Padres closer Huston Street (2-1) that tied the game at 5-5.
Then, after Francisco Peguero reached with an infield hit, Pence pounded a Street pitch over the wall in the decisive blow for the National League West champions.
Chase Headley, Logan Forsythe Yasmani Grandal all homered for the Padres.
Costly malfunction causes beer flood at Boston-area brewery
Wisconsin business offering 'therapeutic cuddling' forced to close