Ryan Theriot and Adron Chambers came up big hit situations in the seventh, as the playoff-seeking Cardinals out runs in the frame to upend the Mets, 11-6.
Theriot doubled in a pair and Chambers hit a bases-loaded triple for St. Louis, which has won six of seven to stay in the NL wild card hunt. The front- running Braves also won on Tuesday, keeping St. Louis 2 1/2 games behind.
"I'm just happy I was able to come up here and help out," said Chambers. "I bet any of these guys in here would love to be in that situation, to get the big hit and get the win."
Angel Pagan had three hits and an RBI to lead New York, which did St. Louis a favor over the weekend by taking two of three in Atlanta.
"It's the same thing we've been watching all year," said New York manager Terry Collins. "We battle back and then we give it right back."
The opener of this three-game set was decided by the bullpens after Jackson and Mike Pelfrey each gave up five runs. Jackson only last five frames and yielded nine hits and four walks, while Pelfrey lasted six despite allowing 10 hits.
Chambers, in his fourth career at-bat, stepped up against D.J. Carrasco following an intentional walk to Yadier Molina and laced a line drive into the right-field corner to clear the bags.
Nick Punto added an RBI single to cap the six-run frame, and the Cardinals held on from there.
Lucas Duda doubled in Reyes in the first inning, and the Mets tacked on three more in the third. Reyes started the inning with a walk and moved to third when Jackson threw away Pagan's bunt back to the mound.
Jackson shook off the rough inning by helping himself in the bottom half with a leadoff single. The starter then raced around from first on a double into the left-field corner by Rafael Furcal, who later scored on a Pujols groundout. David Freese's RBI double two batters later cut the deficit to 4-3.
Pelfrey knocked in a run in the fifth, but gave up a game-tying, two-run single up the middle to Berkman in the bottom half.
Pujols has seven multi-hit games in September, raising his batting average from .286 to .304. He needs to knock in three more runs to reach the 100-RBI mark for the 11th time in his 11-year career..The Mets went 3-for-13 with runners in scoring position and stranded 13.