Bruntlett's triple play preserved a win for Pedro Martinez in his return to New York and quashed a Mets rally against closer Brad Lidge.
With runners on first and second in the ninth inning, Jeff Francoeur hit a line drive up the middle that appeared headed toward center field for a single. But both runners were stealing on the pitch, so Bruntlett was in perfect position as he moved over to cover second base.
He caught the liner easily, stepped on second to double up Luis Castillo and then turned to tag Daniel Murphy for the third out. Murphy tried to backpedal away from Bruntlett, but had nowhere to go.
"Frenchy hit it on the screws," Murphy said. "It happened so fast there was nothing I could do."
After bolting out of the box, a frustrated Francoeur stopped in his tracks and threw down his helmet with both hands.
"What a bizarre ending. I don't know what happened there. The game's over, so I'm happy with that," Lidge said. "That was pretty exciting. That's definitely not the way you draw it up."
The Phillies raced onto the field to congratulate Bruntlett after the stunning ending gave Lidge his 25th save in 33 chances.
It was the first unassisted triple play since Cleveland second baseman Asdrubal Cabrera turned one in the fifth inning on May 12, 2008, against Toronto.
Bruntlett, who made an error earlier in the inning, started at second because All-Star Chase Utley was rested.
Another Phillies second baseman, Mickey Morandini, turned an unassisted triple play in 1992.
It was the first time the Mets were involved in such a play. "Even with the runners going I did not expect him to be there. The only place he could catch the ball was where he was," Francouer said. "To end the way it did was a little disheartening."
Of the 15 unassisted triple plays in big league history, all but one came during the regular season. Cleveland second baseman Bill Wambsganss turned the rare trick in the 1920 World Series against Brooklyn.
Lidge came on in the ninth with a three-run lead, but the first two batters reached on errors.
Angel Pagan, who homered twice - including an inside-the-park shot leading off the first inning - sped all the way to third when his sharp grounder got through first baseman Ryan Howard. Pagan then scored as Castillo reached on a grounder that Bruntlett bobbled for an error.
Murphy followed with an infield single up the middle that went off the glove of a sliding Bruntlett, bringing up Francoeur.
Martinez batted before throwing a pitch. The Phillies scored six times in the first inning off Oliver Perez on three-run homers by Jayson Werth and Carlos Ruiz.
The Citi Field crowd of 39,038 stood and cheered as Martinez walked to the plate in the Phillies' road gray-and-red uniform, a jarring sight for sure after he spent the previous four years with the Mets.
Martinez worked the count to 3-0 and Mets manager Jerry Manuel came out to remove Perez, bothered recently by a tender right knee that sidelined him earlier this season. The move got a loud ovation, and Perez (3-4) was soundly booed as he walked off the field having thrown 47 pitches - 20 strikes - and getting just two outs.
Nelson Figueroa came on and struck out Martinez to end the 26-minute inning.
The 37-year-old Martinez's walk to the mound in the bottom half went mostly unrecognized by the stunned crowd, and he was greeted by Pagan with an inside-the-park homer.
Pagan's drive to left-center got stuck under the padding of the wall briefly. Center fielder Shane Victorino threw his hands up, looking for a ground-rule double, as Pagan slowed into third, but second base umpire Rob Drake allowed play to go on and Pagan raced home for his first career inside-the-parker and second leadoff homer of the year.
Martinez (2-0) never lived up to the $53 million contract he signed with the Mets after 2004, winning just 32 games and missing the 2006 playoffs with one of many injuries, including major shoulder surgery that limited him to just five starts in '07 - all during the September collapse.
The wiry three-time Cy Young Award winner was not offered a contract after going 5-6 with a 5.61 ERA in 20 starts for the Mets last year - a trying season in which his father died.
He labored through six innings - and hit an RBI single - while giving up four runs and seven hits in his third start with the Phillies after signing with them as a free agent on July 15. He struck out five.
Phillies manager Charlie Manuel was ejected in the ninth after umpires reversed a call.
NOTES: Injured pitchers Clay Condrey (left oblique strain) and J.C. Romero (left forearm strain) will both throw at the Phillies' complex in Florida on Monday. ... Pagan's inside-the-park homer was the 25th in Mets history, and second such leadoff shot. The other one was hit by Charlie Neal in May 1963 at the Polo Grounds against Philadelphia. ... Pagan has two multihomer games.