T.J. Ford scored 18 points for the Pacers (1-1), who bounced back from a 105-71 loss to New Orleans on Wednesday for their first preseason victory.
Tyrus Thomas had 15 points and 10 rebounds and Aaron Gray added 13 points and 11 rebounds for the Bulls (0-2).
Chicago rookie Derrick Rose had 13 points and six assists. He made a 3-pointer with 48 seconds left to cut Indiana's lead to 95-92, but Ford responded with a three-point play at the other end with 31 seconds left to put the Pacers in control for good.
Indiana played without injured starters Mike Dunleavy (knee) and Troy Murphy (left foot), while Chicago played without Ben Gordon (toe) and Joakim Noah (eye).
The game was played at Allen County War Memorial Coliseum, and the crowd was split between Pacers and Bulls fans, though it was officially a Pacers home game. Fort Wayne is 120 miles from Indianapolis and 160 miles from Chicago.
The Pacers led 49-42 at halftime with Marquis Daniels scoring all 13 of his points in the first half.
Chicago tied the game at 52 midway through the third quarter, then controlled the rest of the period to take a 74-68 lead.
The Pacers tied the game at 76 on a dunk by Josh McRoberts, and Indiana regained the lead on a reverse layup by rookie Roy Hibbert. He was fouled by Thabo Sefolosha and converted the three-point play to make it 79-76 with just under eight minutes to play.
Sefolosha hit a 3-pointer to give Chicago an 84-81 lead, but a driving reverse layup by Rush gave the Pacers an 86-84 lead, and they never trailed again.
The Pacers traded F Shawne Williams to Dallas for G-F Eddie Jones, two second-round draft picks and cash earlier Friday. ... The Pacers signed C Jeff Foster to a contract extension on Friday. He has spent his entire 10-year career with the Pacers, averaging 5.0 points and 7.0 rebounds. ... Chicago rookie Elton Brown was issued a technical foul in the fourth quarter. The resulting free throw by Indiana's Jarrett Jack tied the game at 84.