With Nationals right-hander Jordan Zimmermann on top of his game, the early deficit was especially difficult to overcome.
Miller gave up four runs in the first inning and the Braves never recovered, falling 6-1 to the Nationals on Tuesday night to extend their long losing streak in the division rivalry.
The Braves have lost nine straight to the NL East-leading Nationals — including a three-game sweep at Washington last week. This was Miller's first loss to Washington.
Clint Robinson's two-run homer was Washington's biggest hit in the four-run inning.
"I just kind of hung a curveball and the next thing you know, it was four runs, kind of put our team in a hole there," Miller said.
Miller (5-4) began the night 2-0 with a 0.85 ERA in five starts against the Nationals. That success ended quickly.
Danny Espinosa's double drove in Denard Span in the first. With two outs, Wilson Ramos hit a single up the middle to drive in Espinosa. Robinson's homer to right field gave Zimmermann a 4-0 lead before throwing his first pitch.
Miller allowed five runs, four earned, with 10 strikeouts in five innings.
A.J. Pierzynski's throwing error on a rundown between home plate and third base allowed Espinosa, who had three hits, to score in the third.
Zimmermann (6-5) was pulled with two outs in the eighth — the only inning he allowed more than one baserunner. Zimmermann hit Jace Peterson with a pitch before giving up a two-out single to Nick Markakis. Left-hander Matt Thornton ended the inning with Pierzynski's groundout.
"Anytime you get the runs like that early in the game you just pound the zone, throw strikes and let them put it in play," Zimmermann said.
Braves RHP Jake Brigham, making his major league debut, threw three scoreless innings, allowing one hit, in relief of Miller.
"I hate that we lost because I'm walking around with a smile," Brigham said.
Ryan Kelly, also making his major league debut, allowed one run in the ninth. Yunel Escobar, who led off with a single, scored when Ramos hit into a double play.
The Braves won the first game of the season series on April 27 before the Nationals' run of nine straight wins. It matches their second-longest winning streak against any team since their move to Washington in 2005.
The Nationals set a franchise record with 11 straight wins against Seattle from 2005-14. They also won nine straight against the New York Mets from 2013-14.
It matches the Braves' longest losing streak to Washington or Montreal. The Braves lost nine straight to the Expos from June 18, 1972 to June 5, 1973.
Nationals: INF Anthony Rendon took batting practice for the first time since he was placed on the 15-day DL on Friday with a left quad strain. ... 1B Ryan Zimmerman (left foot plantar fasciitis) worked out with Class A Potomac and will be evaluated following another workout on Wednesday. He has been on the DL since June 11.
Braves: 1B Freddie Freeman (bruised right wrist) probably will remain on the DL longer than 15 days. Gonzalez said Freeman's wrist "is just not improving" as the medical staff tries different treatments. Freeman is eligible to be activated on Friday and Gonzalez said he's not sure how much more time Freeman will need.
Nationals: Doug Fister (3-3) will look for his second straight win over rookie Matt Wisler and the Braves when the series continues on Wednesday night. Fister threw seven scoreless innings, allowing only four hits, in a 7-0 win at Washington on Thursday.
Braves: Wisler (1-1) will make only his third start since his June 19 promotion. He gave up six runs, four earned, in the 7-0 loss to Fister and the Nationals last week. Wisler was sharp in a win over the Mets in his debut.