With the score tied 2-2, Nick Hundley led off the seventh with a single, went to second on Everth Cabrera's sacrifice and scored when Amarista looped a double down the left field line.
Andrew Cashner tossed a scoreless eighth and Dale Thayer racked up his fifth save for San Diego, which evened its two-game set with LA.
Cameron Maybin drove in a pair runs for the Padres.
Dan Haren (1-5) was tagged with the loss, allowing three runs on six hits over 6 2/3 frames for the Angels.
Erick Aybar had four of the Angels' six hits and drove in a run with a second-inning triple. He scored a run on a Mike Trout groundout in the sixth.