Lefties Santana (9-6) and Cole Hamels traded scoreless frames through the first six innings. Santana struck out six, walked three and didn't allow a hit until Placido Polanco singled with two outs in the sixth.
Hamels (7-8) had given up five hits heading into the seventh - with nine of his 11 strikeouts - before Francoeur led off with his 11th homer just over the right-center field fence.
Reliever Chad Durbin loaded the bases in the eighth, but escaped by striking out Francoeur on a high fastball.
The Phillies then took their turn to threaten in the bottom of the eighth. Jimmy Rollins and Ibanez singled, with Ibanez extending his hitting streak to 15 games. Santana made a difficult play on Polanco's sacrifice attempt to the third-base side of the mound, then fired to David Wright for a crucial force out.
Mets manager Jerry Manuel then went to Rodriguez. He walked Jayson Werth with two outs, but retired Ross Gload on a grounder to second. Rodriguez then worked a perfect ninth.