Nick Markakis went 4 for 4 and scored three runs as the Braves won for the third time in their last 11 interleague road games.
Batting for Cameron Maybin, Gomes opened the eighth with a drive to center off Blue Jays left-hander Brett Cecil (0-1). It was Gomes' 10th career pinch-hit homer, the most among active players.
Two outs later, Markakis singled and Freeman followed with a second-deck home run, his third.
Cody Martin (1-0) worked one inning for the win, Jim Johnson gave up two runs in the eighth and Jason Grilli finished for his fifth save.
