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.
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