Alonso -- who finished with three doubles, two RBI and two runs scored -- reached on a one-out double in the 12th and went to third on a single by Jedd Gyorko. Scutaro misplayed a grounder by Nick Hundley and Alonso scored, helping Joe Thatcher (1-0) get the win and handing the loss to Sergio Romo (1-2).
Thatcher, the sixth reliever to come in after Eric Stults, pitched out of a jam in the top of the 12th to get the victory. Eric Stults went four innings, allowing five runs on four hits, with one walk and five strikeouts.
The Padres have won three straight on.
Barry Zito went 3 2/3 innings, giving up six runs on six hits with one walk and four strikeouts.
Brandon Crawford hit a three-run home run and Hunter Pence hit a two-run triple for the Giants, who have dropped four straight.