Francoeur did not play in the second game of Tuesday's doubleheader, ending his streak of 370 consecutive games played. It was his first game off since Oct. 1, 2005.
Braves rookie Jair Jurrjens (5-3) gave up only one earned run in seven innings for his second win over the Mets this season. Jurrjens gave up five hits and two runs with two walks and a strikeout.
Mets starter Mike Pelfrey (2-5) gave up six runs on eight hits in four innings.
The rest must have helped Francoeur. He hit his first homer since April 12, a two-run shot in the sixth off reliever Pedro Feliciano.
Mark Teixeira had three hits, including a three-run double, and Chipper Jones hit his 12th homer.
Jones' homer tied him with former Braves outfielder Dale Murphy for 45th all-time with 398 homers.
Francoeur drove in runs with a third-inning triple and fifth-inning single before his homer. Needing a double for the cycle, he hit a soft popup to second base in the seventh.
The Mets took a 1-0 lead in the top of the third when David Wright's single drove in Jose Reyes. But the Braves went ahead on Brian McCann's two-run double and Francoeur's triple.
The Braves, 6-2 against the Mets this season, swept a doubleheader on Tuesday night to open the four-game series.
The Mets (22-22) fell to .500 for the first time since April 25, when they were 11-11 after a home loss to the Braves.
Pelfrey gave up three hits, including Jones' homer, and a walk without recording an out before leaving in the fifth. He gave up eight hits and six runs in four innings. Jones left the game in the seventh after he was hit with a pitch on his right ankle by Scott Schoeneweis, loading the bases. With fans booing the Mets reliever, Teixeira followed with a three-run double for an 11-2 lead.
Carlos Beltran, who had two hits, drove in Wright with a double in the eighth. Beltran scored later in the inning on Carlos Delgado's groundout.
On the injury front, Mets left fielder Moises Alou left the game with one out in the third inning because of a cramp in his left calf.