First-base umpire Dave Rackley called Torres out on the appeal play, thus short-circuiting the Mets' gallant comeback effort.
New York appeared in position to at least tie the game when Torres drilled a drive down the right-field line. But according to Rackley, Torres missed the bag rounding first.
Like Torres, Rackley also watched the replay.
"It looked exactly like what I saw on the field," Rackley said. "He went over the front corner [of the bag] with his toe and it kicked some dirt up onto the base. I wouldn't make that up."
Mets manager Terry Collins begged to differ.
"I get back to the bench and I've got 10 guys telling me he touched the bag," Collins said. "I have never seen that called in the big leagues."
Torres, although upset, remained philosophical about the play.
"He missed the call, what can I say?," he noted. "Nobody's perfect."
Cardinals outfielder Carlos Beltran, watching the play on a TV in a batting cage beneath the dugout, spotted the potential infraction.
"I saw sand come up around the bag area," Beltran said. "I told [manager Mike Matheny], 'Let's try to throw to first. It looked like he didn't touch first base.'"
Matheny called Beltran the game's MVP.
The loss, in front of 40,952 at Busch Stadium, snapped the Mets' three-game winning streak. They have still won seven of their last nine.
New York rallied from 4-0 and 5-2 deficits, but fell just short against the Cardinals, who hold the second Wild Card spot in the National League.
"We battled very, very hard against a team that's fighting for something big," Collins said. "I was very proud of the way we came back and made it a game."
Catcher Kelly Shoppach and infielder Daniel Murphy ripped two-run homers in the seventh and eighth innings, respectively, to fuel the rally. Murphy closed the deficit to 5-4 with his fifth of the season.
Ike Davis then drew a one-out walk and pinch-hitter Jason Bay added a single. But St. Louis closer Jason Motte got Scott Hairston and Shoppach to end the threat.
Ruben Tejada drew a two-out walk after the appeal play in the ninth, but Murphy flied to right to end the contest.
"It was a good fight, we gave ourselves a chance," Murphy said. "But it was still a frustrating loss."
Mets rookie right-hander Collin McHugh (0-1), in his second Major League start, found the going a little rougher than his debut. He gave up four runs on six hits in four innings. McHugh threw seven shutout innings in his first game against Colorado on Aug. 23.
"I didn't have very good command," McHugh said. "I've got to be smarter, it's as simple as that. I put us in a pretty deep hole early on. Hats off to the guys for scraping, but I've got to do better than that."
McHugh gave up a home run to Skip Schumaker in the fourth inning after surrendering two runs on four hits in the previous frame. He struck out just two after fanning nine in his debut.
The New York offense tallied just two runs and five hits off starter Joe Kelly (5-6). Torres followed Shoppach's seventh-inning homer with a triple, but reliever Edward Mujica got pinch-hitter Justin Turner to ground out to end the threat.
The Mets had a couple of early scoring opportunities against Kelly. Davis ripped a one-out double in the fourth, but Kelly retired Lucas Duda and Mike Baxter to end inning. Murphy singled with one out in the first and Baxter had a one-out single in the second.
New York reliever Robert Carson had a string of six scoreless outings snapped when he gave up a run in the seventh. Carson hit Jon Jay with a pitch and then struck out Matt Carpenter. Bobby Parnell then gave up singles to Matt Holliday and Allen Craig.
The Mets have been unable to score a run in the 11 innings that McHugh has worked.
The Cardinals nicked McHugh for one run in the first. Jay led off with a line-drive triple that just eluded Duda in left. Carpenter brought in the run with a grounder to second.
Kelly started the two-run uprising in the third with a double.
"That was a bad pitch," McHugh said. "I left it over the middle of the plate, and he got the barrel to it. I put myself in a hole."
After a pair of sacrifices, McHugh gave up successive hits to Holliday, Craig and Yadier Molina.
The Mets, who are 5-2 on their current nine-game road trip, will send Matt Harvey to the mound against left-hander Jaime Garcia on Tuesday in the middle game of the three-game set.