Cory Jefferson scored 23 points and Isaiah Austin had 15 points and nine rebounds for the Bears (23-14), who reached the tournament final five years ago, but never had won it before.
Mike Gesell led Iowa (25-13) with 13 points and Aaron White had 12. Hawkeyes start Devyn Marble was held to six points.
Baylor reached the title game with a disjointed, but ultimately winning, effort against BYU in Tuesday night's semifinal. The Bears looked much more complete on Thursday night.
Jefferson threw down two rattling dunks in the first eight minutes of the half as the Bears slowly pulled away. From Eric May's layup two and a half minutes into the half until Jackson made a 3-pointer with 13:5 1 to play, the Bears went on a 14-4 run.
Jackson made a 3-pointer with 10 and a half minutes to play that put the Bears up 49-34, and the Bears never looked back.
After using a fast start and its characteristically tough defense to beat Maryland in the semifinal, Iowa began the second half on the wrong foot and spent most of the period just trying to keep pace. The Hawkeyes began the second half almost completely unable to make a basket, too, missing eight of their first 10 shots and 11 of 14 after the break, while Baylor pushed its lead out to double digits.
Iowa kept it close in the first half, going into the break down only five points despite being outshot 44 percent to 25 by Baylor.
Jackson led the Big 12 in scoring and assists, the first major-conference player to lead his league in both since Jason Terry did it at Arizona in 1998-99. He also finished his career with at least one 3-pointer in 48 straight games.
Just reaching the semifinals, let alone the title game, was a first for Iowa's program. Baylor lost the NIT title game to Penn State in 2009.
Baylor's A.J. Walton left with an apparent injury to his right leg or foot after colliding with May with about three minutes to play. Shortly after that, Iowa coach Fran McCaffery took May out of the game and the Iowa fans at Madison Square Garden gave him an ovation and chanted his name as he sat on the bench, blinking rapidly and staring straight ahead
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