Orlando scored the first nine points of the extra period after Charlotte's D.J. Augustin hit a 3-pointer with 12 seconds left in the fourth period to force the additional 5 minutes.
Charlotte saw its bid for a post-season berth disappear with the loss to Orlando plus a victory by eighth-place Indiana over Washington.
Arenas made 9-of-15 shots and scored 25 points while Brandon Bass added 19 points and eight rebounds for the Magic. Jameer Nelson poured in 18 points and Dwight Howard had 15.
Howard, however, drew his 18th technical foul of the season and if that is upheld by the league office he will be hit with a one-game suspension.
Gerald Henderson had a career-best 32 points for the Bobcats.