Philadelphia was 0-51 when trailing after eight innings but got a series of big hits to remain one game in front of Florida for the National League wild card berth.
Ex-Met Todd Pratt led off the bottom of the 11th with a single but was forced at second after pitcher Dan Wheeler (1-3) fielded an attempted sacrifice by Tomas Perez. Kelly Stinnett, another former New York catcher, blooped a single inside the right field line that sent Perez to third.
"I didn't know really where the ball was," said Stinnett, who was acquired last week from last-place Cincinnati. "Got Tomas to third base and it got us in a situation where a sacrifice fly could win the game."
"It was great, (gave us) momentum going into Atlanta," Byrd said. "We're still one game up instead of being tied. We have four crucial games (against the Braves)."
Rheal Cormier (6-0) struck out two in two scoreless innings for the win, Philadelphia's sixth in a row overall and ninth in 10 games. The Phillies took the season series, 12-7.
Trying to avoid their first four-game sweep against Philadelphia since June 1995, the Mets grabbed a 4-2 lead in the eighth as Ty Wigginton's two-run double capped a three-run rally. Wigginton tied a career high four hits.
The Phillies climbed within 4-3 in the bottom half on a sacrifice fly by Byrd.
David Weathers came on to start the ninth for New York but gave up a leadoff single to Mike Lieberthal. Pinch hitter Jim Thome walked and Pratt sacrificed both runners into scoring position. After Perez was intentionally walked, Nick Punto atoned for an earlier fielding gaffe with an RBI single. Philadelphia left the winning run at third as Michaels bounced into a fielder's choice, forcing Thome at the plate, and Byrd flied out.
The Phils had another chance to end it in the 10th after Jimmy Rollins hit a leadoff double. But he was picked off and thrown out at third.
"We have a play there that you can steal third so you can score on a wild pitch. Jimmy knows you have to make it," Philadelphia manager Larry Bowa said. "Sometimes you try to make a play when you should back off a little bit."
Pratt homered off Al Leiter in the second and Byrd singled in Telemaco in the fifth to put the Phillies in front.
The Phillies now start a seven-game road trip with four games in Atlanta and three in Pittsburgh. Kevin Millwood (14-9, 3.62) will go against Russ Ortiz (18-6, 3.76) in the series opener Monday night.