Chicago won its fourth straight and has captured nine out of 11.
Deng scored 26 points and Derrick Rose added 22 despite being diagnosed this week with two stomach ulcers. Chicago outscored Orlando by 17 points in the third period and led by 12 heading into the final quarter.
Howard made 14-of-20 shots from the field and 12-of-16 from the foul line to go with 15 rebounds, four steals and three blocks. The 40 points were the most he has scored in a game this season, surpassing the 39 he produced Dec. 9 against Portland and again Jan. 13 against Oklahoma City.
It was the second loss in three games for the Magic, who dropped 2 1/2 games behind Miami for the lead in the Southeast Division.