Niese will head back to New York for tests, the latest setback for the left-hander in what he described as "the spring training from hell." He is expected to have an MRI exam Monday, and it's unclear when he might pitch again.
"It's the back of the elbow, which is good," Niese said. "I'm almost 100 percent sure it's nothing serious."
Adam Wainwright had a rocky outing in his third start this spring, allowing three runs and seven hits in 4 1/3 innings for the Cardinals.
Niese first experienced elbow pain during an intrasquad scrimmage two outings ago. Trainers put him on anti-inflammatories, and he didn't have any issues during his first start of the spring Tuesday against St. Louis.
Back discomfort and triceps soreness slowed Niese earlier this spring. Following his first outing, Niese was optimistic he could be ready for opening day, but now that appears unlikely.
"It's frustrating," he said.
Niese, who started the Mets' season opener last year, allowed two runs in two innings and didn't come out of the dugout for the third. He gave up three hits and one walk, throwing 24 of his 35 pitches for strikes.
The left-hander pitched a clean first inning, then allowed two runs on three hits and a walk in the second, when the pain returned. Niese said he wanted to go back to the mound for the third inning, but the Mets didn't let him.
Niese was sidelined last June with a partially torn rotator cuff. He returned in August, going 5-2 with a 3.00 ERA the rest of the way to finish 8-8 with a 3.71 ERA in 24 starts.
Wainwright allowed a two-run homer to Cory Vaughn in the second inning on a fastball that was left up.
"I got my breaking ball over for strikes like I wanted to today," Wainwright said. "I threw some good changeups, good sinking fastballs, and I threw a couple balls in the middle of the plate."
Wainwright also balked home a run in the first.
"Somebody yelled, `Time!' and like an idiot I stopped," he explained.
Vaughn added a two-run single in the sixth, and Daniel Murphy went 3 for 3.
Mets: Niese's latest injury increases the likelihood that Bartolo Colon will start on opening day against Washington.
Cardinals: After watching pitcher Joe Kelly get three hits Saturday, Wainwright looked forward to taking a few swings, too. That didn't happen, though, because Sunday's game featured the DH.
"He wasn't happy," manager Mike Matheny said. "I just told him it wasn't our decision, just blamed it on the Mets -- which isn't altogether true."
Mets: First baseman Ike Davis went 2 for 6 with two singles in minor league at-bats. He didn't run the bases, but could appear in a Grapefruit League game soon. Davis has only six at-bats in major league games this spring.
Cardinals: Second baseman Mark Ellis missed his third consecutive game. He didn't participate in pregame running because of general soreness, Matheny said. Ellis did take some cuts during batting practice. He might sit out a day or two but, "only because we are in spring training," Matheny said.
TOUGH TO HANDLE
Mets shortstop Ruben Tejada committed his fourth error in the span of seven games on a routine grounder in the third inning. Tejada did respond with two outstanding plays later in the game, including one that started a 6-4-3 double play to end the third.
After going hitless in his first 10 at-bats this spring, Wong is 10 for 20 with four extra-base hits over his last six games.
"He looks great," Matheny said. "He's been playing very well -- doing everything offensively and defensively."