The Minnesota Twins star received 27 of 28 first-place votes and 387 points in balloting by the Baseball Writers' Association of America.
Yankees teammates Mark Teixeira (225 points) and Derek Jeter (193) followed, while Detroit's Miguel Cabrera drew the other first-place vote and was fourth with 171 points, one point ahead of the Angels' Kendry Morales.
Mauer became the second Twins player to win in four years, following Justin Morneau in 2006.
After missing April with a back injury, Mauer homered in his first at-bat of the season and went on to lead the AL in batting average (.365), on-base percentage (.444) and slugging percentage (.587), the first AL player to top all three categories in the same season since George Brett in 1980.
Mauer set a major league record for highest batting average by a catcher and won his third batting title, becoming the first repeat batting champion since Nomar Garciaparra in 1999-00.
Mauer set career bests with 28 homers and 96 RBIs, had more walks (76) than strikeouts (63) and batted .378 after Morneau's season-ending back injury Sept. 12, helping the Twins overtake Detroit for the AL Central title. He was voted to his third All-Star team and won his second straight AL Gold Glove.
Born in St. Paul, the 26-year-old can leave the Twins and become a free agent after the 2010 season, when he is due to make $12.5 million. Minnesota is expected to try to sign him to a new deal.
Ivan Rodriguez in 1999 had been the only catcher since Thurman Munson in 1976 to win the AL MVP. The other catchers to win in the AL were Mickey Cochrane (1934), Yogi Berra (1951 and 1954-55) and Elston Howard (1963). NL catchers to win were Gabby Hartnett (1935), Ernie Lombardi (1938), Roy Campanella (1951, 1953 and 1955) and Johnny Bench (1970 and 1972).
In addition to Mauer and Morneau, other Twins to win were Zoilo Versalles (1965), Harmon Killebrew (1969) and Rod Carew (1977).
Mauer receives a $100,000 bonus for winning the award, and Cabrera gets $200,000 for finishing fourth. Cabrera's first-place vote came from Keizo Konishi of Kyodo News, a member of the Seattle chapter.
Teixeira led the AL with 122 RBIs and tied for first with 39 homers. Jeter was second to Morneau in the 2006 voting and finished third behind Juan Gonzalez and Garciaparra in 1998.