The Pacers (51-18), who took a 13-game lead on the Bulls (38-31) in the Central Division, went on a 19-0 run in the third quarter.
Carlos Boozer was called for a Flagrant 1 foul with 7:31 left in the third, Roy Hibbert made two free throws and Stephenson made a basket to give the Pacers a 63-45 lead.
DJ Augustin and Jimmy Butler each scored 17 points for the Bulls, who have lost two of their last three games.
The win also gives Indiana a 2-1 series lead over the Bulls. The Pacers will visit Chicago on Monday.