Lee finished ninth in the balloting by the Baseball Writers' Association of America with 66 total points, while Pujols was a unanimous selection for his third MVP award. Florida's Hanley Ramirez was second, followed by Philadelphia's Ryan Howard and Milwaukee's Prince Fielder.
Lee, who did receive one second-place vote among the 16 cast with his name on them, did set a career high with 111 RBIs in 141 games this season and led the team with a .306 batting average. The first baseman hit 35 home runs, his highest total since belting 46 in 2005. In 2005, Lee finished third in the MVP balloting.
He's the fifth Cubs player to have two or more seasons with a .300 average, 30 homers and 100 RBIs, joining Hack Wilson (1927-30), Ernie Banks (1958-59), Billy Williams (1965, '70, '72) and Sammy Sosa (1998, 2000-01).
Sosa was the last Cubs player to win MVP honors, doing so in 1998.
Lee, 34, finished fifth in the NL in RBIs, eighth in homers and ninth with 308 total bases and 73 extra-base hits.
Carrie Muskat is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.