Brady claimed 40 of the 50 votes from a national panel of media, with the Los Angeles Rams' Todd Gurley garnering eight votes and Philadelphia's Carson Wentz getting two.
Injured Patriots teammate Julian Edelman accepted the award on Brady's behalf at the NFL Honors ceremony in Minneapolis.
The award is Brady's third MVP honor, tying him with Jim Brown, Johnny Unitas and Brett Favre for second most all-time. Peyton Manning holds the record with five.
Brady thanked his team mates in an acceptance video posted to the Patriots' Twitter account after he received the honor.
"I'm very humbled and honored to accept this award tonight," Brady said. "In a team sport like football, you certainly can't achieve anything as an individual without incredible teammates and incredible coaches who have really committed so much to our team this year."
It was the 10th time in the past 11 seasons that a quarterback won the award, a streak broken only by Adrian Peterson in 2012. A different QB has won it in each of the past five seasons. Brady previously won it in 2007 and 2010.
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The 18-year veteran led the NFL in passing attempts (581), yards (4,577) and yards per game (286.1) this season while throwing for 32 scores and eight interceptions. Only Alex Smith (104.7) and Drew Brees (103.9) finished with a better passer rating than Brady's 102.8.
On Sunday, Brady will try to be the first player to win MVP and the Super Bowl in the same season since Kurt Warner did so in 1999. The last eight MVPs to appear in the Super Bowl wound up on the losing team, including Brady in 2007.