Jeff Francoeur also had a sacrifice fly for New York in the 19th inning, snapping a scoreless tie, but Yadier Molina singled in Albert Pujols with two out in the bottom half.
Francisco Rodriguez (1-0) got the win despite yielding the tying run in the 19th and starter Mike Pelfrey finished for his first career save in a game that included 19 pitchers and lasted 6 hours, 53 minutes.
It was the longest game in the majors since Colorado beat San Diego 2-1 in 22 innings on April 17, 2008.
St. Louis left the bases loaded in the 10th, 12th and 14th and stranded 22 runners, including 14 in extra innings. Molina caught the whole game and went 3-for-9.
It was the longest scoreless game in the majors since the Los Angeles Dodgers and Montreal Expos went 21 innings without a run on Aug. 23, 1989, according to STATS LLC. The Dodgers won that one 1-0 on Rick Dempsey's leadoff homer in the 22nd.
Utilityman Joe Mather (0-1) became the first position player to lose a game since shortstop Josh Wilson for the San Diego Padres in a 9-6 setback in 18 innings against the Arizona Diamondbacks last June 7.
Mather hit for Colby Rasmus in the 10th and played center and third before taking the mound in the 20th for his first major league pitching appearance.
The Mets jumped all over him.
Angel Pagan started the 20th with an infield single and advanced to third on Mike Jacobs' base hit to right. Reyes followed with a fly ball to center field to give New York a 2-1 lead.
Johan Santana started the game for New York and struck out nine in seven innings, allowing just four hits.
Rookie left-hander Jaime Garcia gave up just one hit in seven innings for St. Louis — a bloop single by Pagan leading off the sixth. Infielder Felipe Lopez also pitched a scoreless inning for the Cardinals.
Notes
Pujols walked four times, two intentionally. … St. Louis pitcher Adam Wainwright and Molina were presented their Gold Glove awards before the game. Pujols will receive his NL MVP award and Silver Slugger bat before Sunday's game. … Mets 3B David Wright walked twice, giving him a major league-leading 16 total. … Cardinals OF Matt Holliday, mired in an 0-for-16 slump, struck out three times. … Reliever Pedro Feliciano made his 373rd appearance with the Mets, moving into fourth on the club's career list.