ATLANTA (AP) -- Fredi Gonzalez's bench already was thin when he used Jordan Schafer as a pinch-runner with two outs in the 10th inning.
The decision to utilize Schafer's speed made the difference.
''At the end of the day, you've got to use all the bullets you can,'' said Gonzalez, the Atlanta manager.
Chris Johnson singled with two outs off left-hander Jerry Blevins (1-1), and Schafer pinch ran. With a 2-2 count, Schafer ran on the pitch and Upton dropped a single in front of Bryce Harper.
Schafer already was rounding third when Harper bobbled the ball. No error was charged.
''I've seen Schafer run before,'' Upton said. ''He had a chance after the ball got down and got away from him a little bit. That's why we had speed at first base.''
Blevins threw to first base, trying to keep Schafer close, before Upton's hit.
''They put him in the game to steal second base right there,'' Nationals manager Matt Williams said. ''Otherwise they wouldn't want to lose Johnson. We just want to try to prevent that as much as possible.''
Luis Avilan (2-1) pitched around two walks, one intentional, in the 10th.
Upton hit a solo home run in the eighth off Tyler Clippard that tied the score 6-all, his third homer in two games. Gonzalez said Upton had ''about as pretty a swing as you're going to see'' on the homer to center.
Upton, who had three hits, is hitting .324. He has 10 hits in his last 21 at-bats.
Denard Span's single off David Carpenter drove in Harper in the eighth to put the Nationals ahead 6-5.
Atlanta burst ahead with a four-run second against Tanner Roark, who allowed five runs and five hits in 4 2-3 innings. He hadn't pitched since a win over the Mets on April 4.
Roark, who hit three batters with pitches, said he wasn't affected by the unusually long layoff.
''No, I felt great out there,'' Roark said. ''I just didn't really have the command of my pitches that I wanted.''
Julio Teheran couldn't hold the lead, giving up five runs - two earned - and 10 hits in six innings. Ian Desmond had a run-scoring single in the fourth, when the Nationals left the bases loaded.
Williams used his appeal in the seventh inning when Adam LaRoche was called out at the plate when trying to score on Jordan Walden's wild pitch with Harper batting. The pitch bounced away from catcher Evan Gattis toward the Nationals dugout. Gattis finally spotted the ball and threw to Walden, who made the tag. Plate umpire Adrian Johnson's call was confirmed in the video review.
Braves closer Craig Kimbrel struck out Jayson Werth, Adam LaRoche and Zimmerman in the ninth. Washington's Drew Storen fanned Pena, Ryan Doumit and Jason Heyward in the bottom of the inning.
Pena made his second straight start for shortstop Andrelton Simmons, who jammed his right wrist in a home-plate collision on Wednesday night.
''I don't want something small to become something big,'' Gonzalez said.
If the game had continued to the 11th, Simmons would have entered at shortstop with Pena moving to third base.
NOTES: Williams said Werth left the game with ''a little bit of tightness'' in his groin before the bottom of the 10th. Werth will be evaluated on Saturday. ... Nationals RHP Doug Fister (DL, back muscle) threw 35 pitches in the bullpen before the game. ''He was really impressive,'' Williams said. ''The ball had good life.'' Williams said Fister will go on a minor league injury rehabiliation assignment after he increases his pitch count in bullpen sessions. ... Roark hit Freeman, Uggla and Upton with pitches. ... Simmons was presented his 2013 Gold Glove and Platinum Glove Awards by Rawlings in a pregame ceremony. ... The 10 hits allowed matched Teheran's career high, also against the Nationals on April 29 last year. ... Braves LHP Alex Wood is to face Nationals RHP Taylor Jordan in the second game of the series on Saturday night.