The Braves scored all their runs after the sixth inning to rally from a 4-0 deficit and win their seventh in a row. Washington had a three-game winning streak snapped. The Nationals lost at home for the first time in seven outings this year.
Atlanta trailed by two heading into the ninth and the Braves were down to their final out with the bases loaded when Justin Upton came to the plate.
Upton hit a grounder to third baseman Ryan Zimmerman and his throwing error allowed two runs to score -- forcing extra innings.
After Dan Uggla drew a one-out walk in the 10th off Craig Stammen (2-1), Pena hit his homer to right.