The junior guard, the nation's fourth-leading scorer at 25.8 points per game, exited after just three scoreless minutes due to lower back tightness.
Howard took two of Marquette's first three shots before going to the sideline and attempting to stretch out his back, but he never returned. Howard had a career-high 53 points at Creighton on Jan. 9 to set a school and Big East scoring record.
"I'm not sure how serious it is,'' coach Steve Wojciechowski said about Howard's back. "He's been experiencing some low back soreness. I'm not going to put a guy out there unless he's 100 percent, especially Markus. We wanted to give it a try and he did not look like Markus, so we're not going to put him in jeopardy.''
The Associated Press contributed to this report.