The hot-hitting Ibanez clubbed a hanging knuckleball from Mets starter R.A. Dickey off the batter's eye during the Phillies' big inning. Jayson Werth had three hits, including a solo homer, and Brian Schneider and Ross Gload also drove in runs for Philadelphia.
Halladay (14-8) struggled on an 88-degree afternoon - at least by his standards - allowing five runs on nine hits in seven innings. Phillies closer Brad Lidge worked around a leadoff single by Josh Thole for his 14th save in 18 opportunities.
Dickey (7-5) failed to go at least five innings for the first time in 16 starts. He allowed six runs - four earned - in three innings.
Halladay had allowed one run of fewer in five of his six outings, posting a 1.50 ERA during that span. He retired 12 of 13 batters following a first-inning single by Ike Davis, before Jose Reyes began the sixth with a double and scored on Angel Pagan's single.
New York made the score 6-5 in the seventh on an RBI groundout by rookie Ruben Tejada and pinch double by Chris Carter, before the Philadelphia bullpen shut down the Mets.
Carlos Beltran struck out three times and has just two hits in his last 20 at-bats. New York struck out 11 times each on Saturday and Sunday.
New York came out aggressive against Halladay. Reyes began the game with a slicing line drive and stretched it into a double against right-fielder Ben Francisco. Reyes then perfectly read Pagan's floater over second base, and raced around to score the game's first run.
Pagan would then steal second and third, and scored on an infield hit by Davis.
Werth homered in the second inning before Philadelphia scored five times in the third inning. Ross Gload's single brought in Jimmy Rollins, and Ibanez followed with his three-run shot. Schneider added an RBI single later in the inning.
Notes: Phillies CF Shane Victorino (left abdominal strain) will begin a rehab assignment on Tuesday at Triple-A Lehigh Valley. ... Ibanez batting .407 during a 16-game hitting streak.