Devin Harris had 28 points and 12 assists, and Brook Lopez added 19 points and 12 rebounds for the Nets, who ended their four game winning streak.
While the Magic played its third consecutive game without Nelson, New Jersey guard Vince Carter missed the game with a hyperextended right elbow.
The Nets suffered most without their star.
Scrambling to keep pace with the high-scoring Magic, New Jersey relied heavily on Harris. His three-point play with 3:24 left in the third quarter cut Orlando's lead to 74-64. But moments later Nets coach Lawrence Frank received a technical foul for arguing a call against forward Sean Williams, helping the Magic score the final five points of the quarter.
Ryan Anderson and Jarvis Hayes hit consecutive 3-pointers to trim the Magic's lead to 88-79 with five minutes remaining. The team's traded baskets before the Magic opened up from beyond the arc, with Pietrus making a pair of 3-pointers over the final minutes to put the game away.
But it was Orlando's size that gave the Nets fits throughout.
Howard had seven straight points, and reserve center Tony Battie added seven points in the second quarter to help Orlando take a 59-45 lead at the half. Harris was perhaps the only reason the Nets were able to keep it close, scoring 18 first half points.
New Jersey was playing behind from the start.
Rashard Lewis capped an 11-0 Magic run with a 4-point play to help the Magic take command early, ending the opening period ahead 32-18. Lewis was fouled on the 3-point shot by Hayes, pumping immediate energy into the home crowd.