McGruder finished with 18 points for the Wildcats, who won their fifth straight game and ninth in 10 to maintain a share of the Big 12 lead with sixth-ranked Kansas with two regular season games left. The Jayhawks got their 13th league victory earlier Saturday, 91-65 over West Virginia.
Pierre Jackson had 18 points and seven assists for Baylor, which has lost seven of its past 10 games.
"I don't remember losing on a buzzer-beater — ever. So I don't know how to react to it," said Jackson, who made five straight free throws down the stretch.
Cory Jefferson had 14 points while Isaiah Austin had 11 points and 12 rebounds for his 10th double-double this season.
Baylor is 1-7 in games this season settled by five points or fewer. The Bears had lost by 20 points at Kansas State two weeks earlier.
"It gets old, the same thing over and over," Jackson said. "But you can't really do too much about it. Tonight, I think we played well, we played better than we did the last game. We just played against a real good team tonight. As y'all saw, they won by a hair."
The Bears have a quick turnaround, with a game Monday night at Texas. They close the regular season at home next Saturday against Kansas.
Baylor wore its special neon yellow uniforms unveiled earlier this week by Adidas, including camouflage-patterned shorts in the same bright color. The Bears were one of six teams to get special uniforms for anticipated tournament appearances.
On top of that Saturday, Baylor gave out 10,000 T-shirts to the fans in the highlighter color, brightening up the Ferrell Center.
Until the gloomy finish.