Freeman hit a sharp grounder that was fielded by first baseman Hector Sanchez who threw to second base for the second out. Shortstop Brandon Crawford then threw to first to complete the double play. But the replay review showed Giants pitcher David Huff missed the first-base bag as he attempted to swipe it with his right foot after catching Crawford's throw.
As a result of Freeman being ruled safe, Tyler Pastornicky scored what proved to be the game's final run. Pastornicky was on third base when the disputed play began.
"Yesterday, the replay got us. Today we got two runs [with replay]," Gonzalez said. "The umpire had the right call at home plate and then he didn't tag first base and we got a run. At the end of the day, the system works. It's just awkward how you get to that spot."
During Monday's series opening loss, the Braves saw a seventh-inning threat silenced when Bochy successfully challenged Dana DeMuth's ruling that B.J. Upton had stolen third base with the game tied 1-1 in the seventh inning.
Gonzalez has been successful with each of the five challenges he has requested this year.
Mark Bowman is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.