Pujols, who reached base in each of the Cards' first 39 games, had started all but one of them. St. Louis, in the midst of a stretch of 36 games in 37 days, next has an open date on May 22.
Center fielder Rick Ankiel moved to Pujols' usual No. 3 spot in the batting order, while Duncan batted fifth. Ankiel hit his seventh home run of the season in the first inning on Monday.
Pujols, who is 2-for-11 in his career against Brewers starter Dave Bush, would be available to pinch-hit, La Russa added.
Duncan, who came up playing first base but usually plays the outfield, said he was ready to go.
"It's something I've worked hard at," Duncan said. "It was my original position, so I feel comfortable there. Hopefully I can fill in and do a good job."
The Cardinals came in ranked eighth in the National League in runs scored, and Pujols, who came in fourth in the National League in hitting and leading in on-base percentage (.500), obviously is a big reason why.
"We're not the same team without him," Duncan said. "He's one of the best players in the game. He can't play every game all of the time. Sometimes he needs a rest, and we have guys who can fill in and do a good job."
Pujols had been resisting La Russa's overtures to rest, but Duncan said taking time off is crucial over 162 games.
"It's a long season, and a guy like Albert -- he plays so hard, and is on base a lot -- sometimes you just need a physical break," Duncan said. "That way he can stay fresh down the stretch."
David Brown is a contributor to MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.