Pena's run-producing out put Atlanta ahead after Gerald Laird's RBI single earlier in the frame had erased a 2-1 deficit.
Chris Johnson and Jordan Schafer each later added an RBI as the Braves staged their third straight come-from-behind win against the Dodgers, sweeping the series in a game that was delayed twice by rain.
The late rally handed a victory to Luis Avilan (2-0), who tossed a scoreless eighth inning, while Craig Kimbrel struck out the side in the ninth for his 14th save.
Los Angeles closer Kelvin Jansen (1-3) absorbed his second loss in two games.
Adrian Gonzalez drove in two runs for the last-place Dodgers, who fell to eight games under .500 (17-25).