Korie Lucious added 16 points and Niang Georges 15 for the Cyclones (18-8, 8-5 Big 12).
Pierre Jackson scored 30 points and Cory Jefferson had 15 points and 10 rebounds for Baylor (16-10, 7-6).
After doing damage from behind the arc, Iowa State took advantage of a Baylor defense roaming the perimeter. After two free throws gave the Cyclones a 74-67 lead with 3:47 remaining, their next four baskets were scored in the paint, including two layups and an alley-oop dunk by McGee.
Isaiah Austin hit a 3-pointer for Baylor to make the score 84-79 with 23 seconds to play. After a missed Iowa State free throw, Jackson was fouled with 13.7 seconds left, but missed both free throws.
Jackson, who scored in double figures in 31 consecutive games before being held to seven points in a loss to Kansas State on Saturday, scored 10 points in the first 10 minutes on Wednesday.
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