Harris was ejected early in the second half Saturday after hitting Kramer in the nose with an elbow and temporarily knocking him out.
The Boilermakers (No. 17 ESPN/USA Today, No. 16 AP) then rallied behind their captain for a 67-49 victory, outscoring Michigan 40-20 after the foul by the Wolverines' top scorer.
"We don't retaliate, we just get 'Ws'," Kramer said.
Kramer remained on the ground after the hit, and trainers attended to him for several minutes. Kramer said the team doctor believes his nose is broken.
"I was out, then I woke up and there was a pool of blood around me," he said.
As he stood near halfcourt with a bloody towel over his face, he raised his right arm several times to fire up the crowd before leaving the court for treatment.
Michigan coach John Beilein told the referee he thought an ejection was unwarranted.
"He thought Manny threw his elbow into Kramer's nose," he said. "I argued that he was just transferring his position. Kramer is such a great defender and plays on people so tightly, but Manny was just trying to transfer his position."
Kramer, wearing a protective mask, returned to thunderous applause with 14:53 left in the game.
Purdue's Robbie Hummel made a 3-pointer with 12:12 left to give the Boilermakers a 40-34 lead. Hummel made another 3 to make it 49-36 with just under nine minutes to play and Purdue went on to lead by as many as 20 points.
"We just tried to lock down on defense and just move the ball and get even better shots than we were, and once we got going, just really trying to push that lead out," Kramer said.
E'Twaun Moore, who led Purdue (17-4, 6-2 Big Ten) with 17 points, said Kramer's return gave the team a lift.
"That was definitely good," he said. "I was like 'Dang, he came back?' It was just a little cut, I knew he'd be all right. He's a tough kid. But it was great to see him come back, and we knew he'd have some fire."
Harris, the Wolverines' leading scorer at 17.8 points per game, finished with five points on 2-for-7 shooting and committed five turnovers, primarily with Kramer guarding him. It was the third time in four games Harris was held to fewer than 10 points.
Michigan (14-8, 4-6) played without guard Zack Novak, who was suspended for this game after being ejected for throwing a flagrant elbow in a loss to Ohio State.
Hummel scored 13 points and JaJuan Johnson added 11 points for the Boilermakers, who won their sixth straight.
Purdue, which leads the nation in field-goal percentage defense, held Michigan to 36 percent shooting.
Purdue held Michigan scoreless for nearly seven minutes to start the game, but managed just a 4-0 lead. Michigan recovered and took a 15-13 lead on a basket by Shepherd.
The Boilermakers lost the ball seconds before halftime when Hummel couldn't reach an inbounds pass from Kramer. Michigan quickly moved downcourt for a shot, and Zack Gibson's two-handed tip-in at the buzzer gave the Wolverines a 26-25 lead.
Purdue coach Matt Painter was issued a technical foul for arguing that Hummel was fouled in the scramble for the pass from Kramer. Hummel, who has had back problems for most of the season, remained on the court for several seconds after the halftime buzzer and did not start the second half.
Painter was pleased with the way his team responded.
"I told our guys at halftime that this was a gut-check game," he said. "We've been in tough, pressure situations before, and I'm proud of my guys."
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