But instead of scoring a fourth run and extending the inning, the Padres' inning ended as home plate umpire Mike Everitt ruled that Scott Hairston, attempting to go from first to third base on Headley's hit, was thrown out at third base before Adrian Gonzalez could score from second base.
The Padres wound up winning, 4-2, to cut their deficit in the National League West to one game with one left to play.
Everitt, in a television replay, appeared in good position to see both plays transpire. The Padres argued briefly as manager Bud Black discussed the play with Everitt before play resumed and the game headed to the bottom of the third inning.
The Padres, who entered Saturday two games back of the Giants in the National League West and one game back of the Braves in the NL Wild Card race, scored two runs off Barry Zito in the first inning and got another run in the third inning when third baseman Pablo Sandoval made a throwing error.
The Padres took the first game of a critical three-game series from the Giants on Friday, 6-4.