Howard scored 45 points and pulled down 23 rebounds. He attempted a stunning 39 free throws as the Warriors consistently chose to put him on the line rather than allow him to score from the field.
The strategy worked to an extent, in that he made only 21 of his attempts, but one of those came at the start of Orlando's surge that concluded the contest.
The game was tied when Howard made a layup with 1:05 to go. He was fouled by David Lee on the shot and the resulting free throw gave the Magic a three-point lead. Von Wafer then hit a 3-pointer with 37 seconds left for a six-point cushion, wrapping up Orlando's third straight win.
The Magic climbed into a share of the lead with Miami in the Southeast Division.
The Warriors missed out on a chance to record back-to-back wins over two NBA powerhouses. Golden State had downed Miami in overtime Tuesday.
Monta Ellis paced Golden State with 30 points and Lee scored 26.
Pregnant Mila Kunis wins 'Best Villain' at MTV Movie Awards
'Happy' fan videos make Pharrell cry [VIDEO]