George Hill finished with 21 points for the Pacers, who put five players in double figures and pulled away with a third-quarter burst.
Roy Hibbert scored 11 and David West 10 for Indiana, which leads the Eastern Conference at 23-6. Stephenson also had nine rebounds and seven assists.
Paul Pierce scored 18 points, Mirza Teletovic 17, Deron Williams 14 and Alan Anderson 10 for the Nets, who fell to 10-20.
Indiana, leading by three points at the start of the third quarter, went on an 11-3 run as the Nets turned the ball over on four straight possessions.
That pushed the Pacers' lead to 72-61 with 8:07 to go in the period, and they maintained their edge throughout.
George hit a 16-foot, pull-up jumper to give the Pacers their biggest lead, 105-89, with 2:15 to play.
The Pacers shot 53.5 percent in beating the Nets for the third time this season. They outscored the Nets 14-2 in the paint in the decisive third quarter and 20-6 in the second half.
The Nets continue their difficult three-game road trip with games in San Antonio and Oklahoma City.
The first half was close throughout, with eight lead changes and five ties. Indiana shot 54 percent before halftime and the Nets made 50 percent.