The Boilermakers (25-6, 14-6 Big Ten) avenged a 68-65 loss to the rival Hoosiers earlier in the season to snap a two-game losing streak. Sasha Stefanovic added 15 points for Purdue with Zach Edey and Jaden Ivey scoring 10 points apiece.
Indiana (18-12, 9-11) suffered another blow to its NCAA Tournament hopes in a must-win game. Indiana rallied from as many as nine points down in the second half, going on an 11-0 run to take a 51-48 lead on a driving layup by Rob Phinisee.
But the Hoosiers were unable to hold an ensuing four-point lead. Stefanovic put Purdue ahead to stay 59-56 on a 3-pointer with 5:10 left.
Down 67-65, Indiana had a chance to take the lead in the closing seconds, but Parker Stewart missed a 3-point attempt with 16 seconds left. Trayce Jackson-Davis was fouled on the rebound, but Indiana turned the ball over on the ensuing in-bounds pass, with Purdue's Mason Gillis coming up with a steal on a pass under the basket from Miller Kopp intended for Jackson-Davis.
Trailing 69-67, Indiana's last-gasp effort fell short when Xavier Johnson missed a 35-foot heave with 0.3 seconds left.
Johnson led Indiana with 18 points and 12 assists, with Jackson-Davis adding 15 points and Kopp scoring 12 points.
Hunter scored 10 points in the first half, helping Purdue take a 33-29 lead into halftime. With the score tied at 14, the Boilermakers went on a 12-0 run, which included a 3-pointer from Stefanovic, five points from Hunter and an inside layup from Edey, which put Purdue up 26-14.
Purdue went up 33-20 on a layup from before the Hoosiers closed the half on a 9-0 run. Johnson scored six of the nine points, including a jumper in the paint with 40 seconds left that cut the Purdue lead to 33-29.
Indiana tightened up defensively late in the first half, holding Purdue scoreless for the final 2:44.
Purdue shot 38.7 percent from the field in the first half but burned Indiana on the boards, outrebounding Indiana 18-15 and outscoring the Hoosiers 8-0 in second chance points.