It was the first post-season championship of any kind for the Baylor men's basketball program and came one year after the women's team from the school had captured its second NCAA title.
The Bears hit 54 percent from the field and held Iowa to 27 percent.
Iowa was within a point 2:30 deep into the second half when the Bears embarked on a 30-12 run over an 11-minute stretch.
Pierre Jackson added 17 points and 10 assists while Isaiah Austin had 15 points for the Bears (23-14). Baylor defeated Long Beach State, Arizona State, Providence and Brigham Young to reach the championship game.
Iowa (25-13) was led by 12 points from Aaron White. Roy Devyn Marble, who had been averaging 24 points a game during the tournament, scored just six points while going 3-of-12 from the field.