Carlos Pena knocked in the go-ahead run and 6.
The Mets stranded 15 runners, including three apiece in the ninth and 10th innings to fall for the fourth time in five games.
Chicago also had trouble with runners on, leaving 12, but came through against Josh Stinson in the 11th.
Marlon Byrd worked a leadoff walk and moved to third on LaHair's base hit. Pena then singled through a shifted infield to bring in Byrd, and Stinson (0-1) was mercifully pulled after walking Colvin.
Ramon Ortiz (1-2) recorded the final two outs in the 10th to earn the win.
The rubber match of the three-game series was preempted by a remembrance ceremony for those lost in the terror attacks on September 11, 2001. Members of the New York City Police Department, New York City Fire Department, and many other first responders participated in the event, during which a 300-foot by 100-foot American flag was unfurled.
Pena tripled in a run in the first inning, and Angel Pagan countered with an RBI double in the bottom half.
The Cubs loaded the bases with a hit batsman and two walks in the third, and Colvin's two-out single brought home a pair.
New York tied it in the eighth. With two down and runners on first and second, pinch-hitter Justin Turner hit a comebacker off Jeff Samardzija's glove, and the ball rolled toward the first-base line. Samardzija retrieved it, but his throw on the run was too low for Pena to handle. Pagan never stopped running and scored without a play at the plate.
Pridie struck out to leave the bases loaded in the ninth, and David Wright flied out to left to strand three an inning later.
"That's baseball," Mets outfielder Jason Bay said. "But it was a little bit different today."
Pena has three triples this year, his most since recording four in 2004...Cubs starter Matt Garza lasted seven innings and was charged with three runs on seven hits....Miguel Batista started for New York and was pulled after yielding four runs on five hits over the first five frames...Mets shortstop Jose Reyes went 1-for-5 to extend his hitting streak to 14 games...This was the Cubs' first series win in Flushing since taking two-of-three from July 24-26, 2006 at Shea Stadium...Game time: 4:28.