The St. Louis Cardinals first baseman ended Barry Bonds' four-year winning streak, receiving 18 first-place votes and 14 seconds for 378 points in balloting by the Baseball Writers' Association of America. Jones, the Atlanta Braves center fielder, got 13 first-place votes, 17 seconds and two thirds for 351 points.
"It's awesome when you hear people compare yourself with Barry," Pujols said.
Pujols was second in the NL with a .330 average, five points behind Lee, and hit 41 homers, trailing only Jones (51) and Lee (46). Pujols tied for second in RBIs with 117, 11 behind Jones.
He played in 161 of 162 regular-season games despite being bothered nearly the entire season by plantar fasciitis, a heel injury that he also felt in 2004.
"There were some times when I got out of bed, I had to sit up before I jumped out of bed because it was bothering me so bad," he said.
The 25-year-old Pujols has put up remarkable statistics in his first five major league seasons, averaging 40 homers and 124 RBIs to go with a .332 average.
He was third behind Bonds and Adrian Beltre in last year's MVP voting after finishing fourth as a rookie in 2001 and second to Bonds the following two seasons. Bonds missed most of this year with a knee injury after winning the award four straight times to increase his total MVPs to a record seven.
Jones led the major leagues in home runs for the Braves, and batted .263. He has won eight straight Gold Gloves.
"I think he deserved it. The voting was the right vote. He was the right choice," Jones said. "He had the most solid season average wise, home run wise and RBI wise."
The Cardinals led the majors with 100 wins this season and breezed to the Central title. Pujols was the driving force on a team that lost Scott Rolen and other key players to injuries.
Atlanta went 90-72 and won its 14th straight division championship. Jones was the only Braves player with more than 21 homers or 78 RBIs.
Pujols, who gets a $200,000 bonus, won the 15th MVP award for the Cardinals, the first since Willie McGee in 1985.
By finishing third, Lee triggered a $750,000 increase in his next 2006 base salary to $8.75 million.
Florida first baseman Carlos Delgado, who was sixth, earned five points toward the 30 he needs by the end of 2008 to guarantee a $16 million salary in 2009. He would get 10 points for winning the MVP, 20 if he is a World Series MVP and 10 if he is a league championship series MVP.