Brad Thompson (3-2) worked two perfect innings for the win.
Struggling Cardinals closer Ryan Franklin blew his second straight save, surrendering a leadoff homer to Fernando Tatis in the ninth inning. Rick Ankiel leaped for it at the wall and crashed to the warning track, and for a moment the entire stadium wondered whether he had caught it.
Ankiel stood up and slapped his empty glove in frustration, and Tatis finished rounding the bases to tie it at 8. It was the fifth homer Franklin has allowed in his last nine outings.
The Mets had several chances to win it in extra innings.
Pinch-hitter Ramon Castro grounded out with runners at second and third to end the 11th, and New York loaded the bases with three straight two-out walks in the 12th before Kelvin Jimenez got Tatis to break his bat on a harmless bouncer back to the pitcher.
The Cardinals stranded 17 runners, the Mets 16.
Troy Glaus, Yadier Molina and Aaron Miles each drove in a pair of runs for St. Louis, which denied the Mets their fourth straight win.
Carlos Delgado hit a pair of homers and finished with three RBIs for New York, which got a gutsy performance from Brandon Knight in his first major league start. Jose Reyes also homered and had two doubles among his four hits a day after getting married.
The game lasted 5 hours, 9 minutes, and the teams combined to use 16 pitchers - 17, if you count Cardinals starter Braden Looper striking out as a pinch hitter in the 13th.
Filling in for Pedro Martinez, who is on the bereavement list following the death of his father, Knight surrendered four runs in the first but shut the Cardinals out over the next four innings and left with a 5-4 lead.
St. Louis went ahead in the sixth. Pujols, Glaus and Molina had RBI singles before Miles doubled in Glaus to make it 8-5, drawing a chorus of boos from the Shea Stadium crowd.
Delgado hit a two-run homer in the bottom half, his 11th in the last 26 games, getting the Mets close enough for Tatis to tie it in the ninth.
Knight allowed seven hits over five innings in his first big league start, and the Mets will have to decide soon whether that's enough to stick around. He was picked for the U.S. Olympic team headed to Beijing in a couple weeks, giving him a unique no-lose situation little more than a year after he considered hanging up his spikes.
Knight looked like he was going to make it an easy decision early on.
Schumaker led off the game with a single, Ludwick got plunked and Pujols snapped an 0-for-11 slump with another hit to load the bases. Ankiel made it 1-0 with a single to left.
Glaus had a bases-loaded walk, Molina added a sacrifice fly and Miles drove in a run with a base hit before Knight finally got Cesar Izturis out on his 39th pitch to end the inning.
Fortunately for Knight, Joel Pineiro struggled even more.
He gave up a pair of runs in the first, two more in the third and the homer to Reyes leading off the fourth. Pineiro wound up allowing 10 hits and has just one win in his last 13 starts.
Notes: Delgado's two homers gave him 453, moving him past Carl Yastrzemski for 32nd place on the career list. ... The Cardinals traded former major league starter Anthony Reyes to Cleveland for minor league reliever Luis Perdomo. ... Cardinals ace Chris Carpenter, out since the 2007 opener because of elbow ligament replacement surgery, is expected to start Wednesday against Atlanta, manager Tony La Russa said. ... Portly Mets C Robinson Cancel stole his first career base in the fifth inning.
