The team's immediate future at the position could bring more surprises.
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X-rays at the stadium showed the broken bone. The Cardinals did not say how long Freese is expected to be out.
"It's a bone on top of another bone type of deal," Freese said, adding he will see a doctor in St. Louis on Monday. "I'll see what they say. Maybe I'll need surgery just to speed up the process."
Gonzalez, who had a two-run homer in the fifth, opened the ninth with a pop fly off Franklin (0-3) that bounced off shortstop Ryan Theriot's glove for an error.
"I just dropped it," Theriot said. "Hit in the palm and I dropped it."
"Terrific effort. Terrific series," manager Tony La Russa said. "But I learned a long time ago, I'd much rather lose a game than lose a player and get a guy hurt. So the worst part is David Freese getting hurt. That's really hard to take for our team and for him."
The Cardinals have other injury concerns. Descalso was in the game because starting second baseman Nick Punto left in the fourth due to tightness in his left hamstring.
Pujols moved from first base to third in the eighth, his first appearance at the position since Sept. 23, 2002, against Arizona.
Jonny Venters (1-0) pitched a perfect ninth for the Braves.
Atlanta starter Derek Lowe gave up six hits and four runs in five innings three days after his DUI arrest.
Lowe was charged with DUI, reckless driving and improper lane change on Thursday night after he was spotted by a Georgia State Patrol trooper racing another car down an Atlanta street.
The Cardinals, who had comebacks to win the first two games of the series, couldn't hold a 4-0 lead. Matt Holliday had a two-run double in the first. Lance Berkman and Pujols added run-scoring singles.
Atlanta's Dan Uggla knocked Jaime Garcia out of the game in the seventh with a drive off the top of the center-field wall. Uggla thought he hit a homer, but the umpires ruled it a double. They confirmed the ruling with a review that lasted 1 minute, 13 seconds.
Gonzalez followed with a grounder to first that Pujols mishandled for an error, allowing Uggla to score for a 4-4 tie. Martin Prado's single off Jason Motte drove in Mather to give Atlanta the 5-4 lead.
Garcia gave up five hits and four runs in six-plus innings.
Lowe settled down with three strong innings before the Cardinals pushed the lead to 4-0 in the fifth when Pujols drove in Garcia with a single up the middle.
After Garcia threw four perfect innings to open the game, the Braves broke through in the fifth on the homer by Gonzalez and pinch-hitter Brandon Hicks' RBI single.
"That inning when I got hurt [by hits], I left a couple pitches up," Garcia said.
The Cardinals couldn't score after loading the bases against Linebrink with no outs in the sixth. Berkman, who led off the inning with a single, was thrown out at the plate on Theriot's grounder to third baseman Chipper Jones. McCann threw to first to complete the double play, and George Sherrill struck out Garcia to end the inning.
- Hicks' pinch-hit single was his first major league hit.
- Punto left the game in the fourth inning due to tightness in his left hamstring. Daniel Descalso replaced Punto at second base.
- The attendance was 34,129, including 559 dogs for Bark at the Park day.