A series of lineup changes were made to accommodate the move, with Scott Spiezio moving from third base to first base, Hector Luna from left field to third base and John Gall inserted in left field.
Pujols first started feeling some discomfort more than a week ago on a play at first base against the Cubs.
"It was pretty tough coming in today," Pujols said on Tuesday. "I wanted to play, but [manager Tony La Russa] told me to be smart with it."
Pujols is likely to return to the lineup on Wednesday night in Houston.
"He jammed it sliding into first base on the homestand," said La Russa. "It's sore. Day games after night games ... it just hasn't responded enough to where he should go out there without risk."
Head athletic trainer Barry Weinberg characterized the condition as a lower back strain. Weinberg said he has been trying to get Pujols to take a day off all week. Pujols is feeling discomfort through much of his lower midsection.
"It's not specific in one spot," Weinberg said. "I think the main episode was he jammed it sliding back into first base on a defensive play. That was the main thing. It's pretty diffuse, not really specific in one spot."
With a left-hander on the mound for Cincinnati, and the Cardinals in the midst of playing on 20 consecutive days, Jim Edmonds also received a day off. Scott Rolen is still recovering from bronchitis, meaning that none of the Cardinals' three heart-of-the-order sluggers were in the lineup. It was the first time since Rolen was acquired from Philadelphia in 2002 that all three players were out of St. Louis' starting lineup.
Rolen's return: Rolen is expected to rejoin the team in Houston, but a date for him to play in a game has yet to be determined. The third baseman stayed back in St. Louis to work out the past two days. He's been out for more than a week with an illness that the team has termed bronchitis.
Rolen worked out for more than an hour on Monday, but inclement weather in St. Louis limited what he was able to do on Tuesday.
"We'll see how he recovers," Weinberg said. "If he got a good workout in today, we'll be optimistic."
Protecting the pitching: As was somewhat expected, the Cardinals added a 12th pitcher on Tuesday, purchasing the contract of right-hander Brian Falkenborg from Triple-A Memphis. Outfielder Skip Schumaker was optioned to Memphis to make room on the roster.
Falkenborg had been brilliant as Memphis' closer. In nine games, the 28-year-old pitched 11 innings, allowing one run on four hits. He struck out 15 batters and walked just one. Falkenborg made a fine impression in Spring Training and was one of the last players sent out.
"[It was] not automatic, but he's the guy that got recommended," La Russa said. "He pitched well enough to earn the call."
Schumaker got off to a strong start, but tailed off at the plate in recent weeks. He hit .179 with a .256 on-base percentage in 16 games. Schumaker had just seven at-bats in the past two weeks.
"You never want to be sent down, but it's part of it," he said. "I knew [Larry] Bigbie was going to come off [the disabled list] eventually, anyway. I wasn't producing like I feel like I should have been, so it was going to be me."
This date in Cardinals history: On May 2, 1957, the Cardinals edged the Dodgers, 3-2, in 16 innings at Ebbets Field in Brooklyn. Don Blasingame's RBI single delivered the winning run. Perhaps the most remarkable thing about the game by today's standards, though, is the showing by Cards starter Herm Wehmeier. The right-hander pitched 12 innings, allowing two runs on nine hits with 12 strikeouts -- but obviously did not receive a decision.
Baby 'Birds: Triple-A Memphis beat New Orleans, 9-4, on Monday, as Dennis Tankersley picked up his first win. Brian Daubach went 2-for-4 with three RBIs. ... Iker Franco reached base three times and scored twice for Double-A Springfield in a 4-2 win over San Antonio. Rich Rundles pitched seven solid innings (two earned runs, five hits, two strikeouts, two walks). ... Sean Danielson singled twice and walked for Class A Palm Beach, which lost, 6-5, to Vero Beach. ... Class A Quad Cities split a doubleheader with Lansing, winning, 6-5, and losing, 1-0. Colby Rasmus went 3-for-4 with a double, a home run and three RBIs in the opener.
The player of the day was Daubach, who is having a big year at Memphis. The veteran first baseman/outfielder, who signed a Minor League contract with the Cards this winter, is batting .340 with a .418 on-base percentage and .553 slugging percentage.
Coming up: It's another two-game series, starting on Wednesday in Houston, but it should be a good one. Jason Marquis takes the mound against Astros ace Roy Oswalt at Minute Maid Park. First pitch is scheduled for 7:05 p.m. CT.
Matthew Leach is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.