Cabrera collected a one-out single in the ninth against Matt Belisle (3-7). One out later, Chase Headley was intentionally walked to get to Alonso, who made the Rockies pay by lining an 0-1 pitch into left field for a solid hit.
Cabrera (three RBI) streaked home and slid around Wilin Rosario's tag for the winning run.
Alonso went 4-for-5 with two RBI for the Padres, who let an 11-5 lead slip away in the eighth inning when the Rockies exploded for six runs, highlighted by Josh Rutledge's score-tying, three-run blast.
Joe Thatcher (1-4) earned the win after getting the final two outs in the top of ninth.
Logan Forsyth added four hits and scored three times for San Diego.
Rutledge ended with four RBI, while Matt McBride socked his first major league homer and pitcher Alex White provided a three-run shot for the Rockies.