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Ryan Ludwick lacked a triple for the cycle and drove in two runs, including Albert Pujols to start the big comeback. Pujols had taken a few menacing steps toward the celebrating Villanueva before being steered away by home plate umpire Phil Cuzzi, and then he answered with a double off David Riske (1-2) to open the eighth.
"When you start pointing to the dugout and saying all the things that he was saying, a guy that respects the game like I myself, I didn't appreciate it and I had to let him know," Pujols said. "I guess he did us a favor. He woke up a sleeping giant."
Rebounding from a 12-0 rout Tuesday, the Cardinals pulled within 3 1/2 games of the Brewers for the NL wild-card lead. That's where they were starting a two-game series that was their final shot against Milwaukee.
The Brewers took the season series 10-5 and had won seven in a row against the Cardinals before Wednesday.
"There's days we're not good enough, but we really try," manager Tony La Russa said. "We have more talent than people think."
The Cardinals were held to four hits in the first five innings and had a scoreless streak of 19 innings against Milwaukee pitching dating to July before Ludwick's 32nd homer off Manny Parra in the sixth. They left the bases loaded in the seventh when Joe Mather fouled out against Villanueva, who celebrated demonstratively while facing the St. Louis dugout.
Villanueva said he was not trying to show anybody up.
"I was caught up in the heat of the moment, got excited a little bit and they took offense to it," Villanueva said. "A couple of words were said back and forth, but I'm not going to be intimidated by anybody.
"I may have looked over there, but I didn't look at anybody in particular."
Like Pujols, Cardinals starter Adam Wainwright thought it was the turning point.
"We had some tempers flare and it probably helped us, it probably woke us up a little bit," Wainwright said. "Sometimes it takes something like that to really get the juices flowing."
Ludwick made it 3-2 with a double to score Pujols in the eighth and scored on a game-tying single by Troy Glaus, who took second on the throw home. After moving to third on a groundout, Glaus slid in just ahead of catcher Jason Kendall's tag with the go-ahead run when shortstop J.J. Hardy short-hopped his throw to the plate on pinch hitter Aaron Miles' grounder against a drawn-in infield.
"You don't have to do stupid things like that to disrespect this game," Pujols said. "Like I said, he did us a favor and we pulled through and I'm glad he did that."
Ryan Franklin (5-5) worked a scoreless eighth with a walk and strikeout and rookie Chris Perez finished for his sixth save in seven chances with three strikeouts in the ninth, allowing only a one-out double to Hardy. Perez is 6-for-6 since being recalled from Triple-A Memphis in early August to replace Jason Isringhausen as the closer.
"This is great. Coming to the ballpark every day and fighting for a playoff spot makes it even better," Perez said.
Hardy had three hits and an RBI for the Brewers, who had outscored the Cardinals 42-7 during their streak. Milwaukee is 58-6 when leading after seven innings and the Cardinals are 5-39 when trailing after seven.
Wainwright allowed three runs, two earned, and threw 89 pitches in his second start coming off the 15-day disabled list from a finger injury that sidelined him for two months. Parra allowed a run on six hits, departing after allowing a single to Yadier Molina to open the seventh.
In the third, the Brewers took a 1-0 lead on three infield hits and a Wainwright throwing error trying to get an out on one of them. They scored when Hardy barely beat out a slow roller to short after Cesar Izturis' barehand grab and throw.
Milwaukee opened the fourth with consecutive doubles by Corey Hart and Mike Cameron, and Jason Kendall added an RBI single for a 3-0 lead.
Notes: Pujols was 2-for-4 and is batting .357, a point ahead of Atlanta's Chipper Jones in the NL batting race. ... La Russa's season-long strategy of batting the pitcher eighth backfired in the second when Molina and Nick Stavinoha singled with two outs and Wainwright grounded out for the third out. ... Josh Phelps, whose contract was purchased from Triple-A Memphis by the Cardinals earlier in the day, had a pinch-hit single off Villanueva in the seventh. ... Ryan Braun was 0-for-4 and hit by a pitch, hitless for only the second time in 13 games against the Cardinals. He still ended with a .459 average, seven homers and 13 RBIs against St. Louis.