The 5-foot-6 Altuve drew 27 of the 30 first-place votes in balloting by members of the Baseball Writers' Association of America.
Altuve batted a major league-best .346. He hit 24 home runs with 81 RBIs, scored 112 times, stole 32 bases and showed a sharp glove at second base.
The 6-foot-7 Judge won the AL Rookie of the Year award Monday. He set a rookie record with 52 home runs.
Jose Ramirez of the Cleveland Indians finished third. The award was announced Thursday.
Altuve helped lead the Astros to their first World Series championship. Voting for these honors was completed before the postseason began.
In the closest MVP vote since 1979, Stanton became only the sixth player to win from a losing team. Stanton led the big leagues with 59 home runs and 132 RBIs (see full story).
MLB: Manfred says pace changes will happen with or without union
Major League Baseball will change rules to speed games next year with or without an agreement with the players' association.
Management proposed last offseason to institute a 20-second pitch clock, allow one trip to the mound by a catcher per pitcher each inning and raise the bottom of the strike zone from just beneath the kneecap to its pre-1996 level at the top of the kneecap. The union didn't agree, and clubs have the right to impose those changes unilaterally for 2018.
Players and MLB have held initial bargaining since summer, and MLB chief legal officer Dan Halem said this week he would like an agreement by mid-January.
"My preferred path is a negotiated agreement with the players, but if we can't get an agreement we are going to have rule changes in 2018 one way or the other," baseball Commissioner Rob Manfred said Thursday after a quarterly owners' meeting.
Nine-inning games averaged a record 3 hours, 5 minutes during the regular season and 3:29 during the postseason.
There are ongoing talks for a new posting system with Japan to replace the deal that expired Nov. 1, one that would allow star Japanese pitcher/outfielder Shohei Otani to leave the Pacific League's Nippon Ham Fighters to sign with a big league team (see full story).
Mariners: Team makes trade, raises available money for Japan's Otani
The Seattle Mariners have gained more flexibility if they want to try to sign star Japanese pitcher/outfielder Shohei Otani.
They acquired an additional $500,000 for their international signing bonus pool from the Chicago White Sox in a trade for Brazilian right-hander Thyago Vieira.
Otani, a 23-year-old right-hander, would be limited to a minor league contract with a signing bonus under Major League Baseball's new collective bargaining agreement. The trade announced Thursday increases the Mariners' available money for a signing bonus to $1,557,500. Seattle has spent $3,942,500 on bonuses in the signing year that started July 2 from a pool that rose to $5.5 million with the trade.
The 24-year-old Vieira made his major league debut with a scoreless inning against Baltimore on Aug. 14, his only big league appearance. He was 2-3 with two saves and a 3.72 ERA in 29 games this year for Double-A Arkansas and 0-1 with two saves and a 4.58 ERA in 12 games for Triple-A Tacoma.
Chicago is restricted to a maximum $300,000 signing bonus because it exceeded its pool in a previous year under the old labor contract.