Howard hit 11-of-14 shots from the field and 8-of-12 free throws in the Magic's fourth win in their last five games.
The Pacers were coming off an overtime loss to Miami Saturday and showed some apparent fatigue as they went 1-for-12 from 3-point range and committed 13 turnovers.
Paul George led the Pacers with 22 points and eight rebounds. Danny Granger added 18 points.
The Magic jumped off to a fast start with a 36-point first quarter but had to hold on when they were outscored by the Pacers 28-16 in the fourth quarter.