Rollins was pulled for the start of the seventh inning after a pair of mistakes in the sixth.
The former NL MVP failed to run hard on a dropped popup that could have put him on second base. He stole second base, then was caught in a rundown on a grounder and was tagged out.
Rollins drew the ire of Phillies fans earlier this month when he jogged down the line on a grounder in a game at Miami. He met privately with manager Charlie Manuel the next day. Manuel refused to bench his All-Star shortstop then. He had no hesitation against the Mets.
Kyle Kendrick (8-9) allowed solo homers in the first two innings to Mike Baxter and Scott Hairston, but did not permit another run before leaving with two outs in the eighth.
Jonathan Papelbon tossed a scoreless ninth for his 30th save as the Phillies avoided a three-game sweep.
Kendrick retired 13 straight starting in the fourth inning and won his fourth straight start. Kendrick has more wins than Cliff Lee (3) and as many as Roy Halladay (8). Kendrick struck out six and walked none.
Rollins got fans talking after his latest baserunning gaffes. He popped up and appeared to be making a turn toward the dugout until pitcher Jonathon Niese dropped the ball for an error and Rollins dashed to first.
With Kendrick on third and Rollins on second, Kevin Frandsen hit a grounder to second. Rollins took off for third with Kendrick staying on the base and was tagged out.
It was the latest blunder in a disappointing season for the Phillies. Rollins has been chewed out and benched by Manuel in the past for not hustling. When he did it twice in one inning, Manuel saw enough and yanked him.
The Phillies are far removed from the franchise that won the last five NL East titles. Their lineup against Niese (10-8) seemed more appropriate for spring training. Ty Wigginton in left and Michael Martinez in right were the starting corner outfielders. Catcher Steven Lerud made his major league debut and Frandsen started at third.
Kendrick left to a standing ovation with runners on first and second in the eighth.
Raul Valdes needed one pitch to retire Ike Davis on a grounder.
Baxter connected on the second pitch of the game for his first career leadoff homer. Hairston hit a solo shot, his 15th, in the second.
Frandsen had an RBI single in the third and Wigginton tied it with a double in the fourth. Ryan Howard's sacrifice fly in the fifth put the Phillies up 3-2.
Niese gave up three runs and nine hits in six innings.
Lerud's bloop single in the fourth was his first career hit after nine years in the minors. The 27-year-old catcher was originally Pittsburgh's third-round draft pick in 2003. He bounced around before getting the call when Brian Schneider went on the disabled list.
NOTES: Phillies INF Hector Luna was outrighted off the 40-man roster and elected free agency. The Phillies are now at 39 players on the 40-man roster. ... The Phillies are 2-7 at home against the Mets this season.