Joe Johnson, who led the Hawks with 26 points, hit a 3-pointer with 1:10 remaining to pull the Hawks to 102-100. Howard responded with a 5-foot turnaround jumper to make it 104-100 with 54 seconds remaining.
Johnson followed with another 3, leaving the Hawks a point down, but the Atlanta star missed a 12-footer with 27 seconds left for the lead. Howard got the rebound and was fouled. He made one of two free throws.
The Hawks had one more chance, but Mike Bibby missed a long jumper with 15 seconds remaining. Rashad Lewis hit two free throws to clinch it, and added two more for the final margin.
"We made some defensive mistakes, such as not contesting Joe Johnson's 3-point attempt late in the game," Orlando coach Stan Van Gundy said. "We have to do a better job, but a game like this is good because we get to see what else we have to work on before the start of the season."
Lewis scored 25 points and pulled down eight rebounds. Teammate Courtney Lee chipped in with 13 points and four rebounds.
Orlando made 30-of-39 free throws and committed 16 turnovers, leading to 22 points for the Hawks.
"Free throws and turnovers are still two glaring errors," Van Gundy said.
Atlanta was up 27-26 after the first quarter, but the Magic opened up a 39-29 lead 4 1/2 minutes into the second quarter. Johnson took over, scoring 10 points in the last 5 1/2 minutes of the half to pull the Hawks to 54-53 at the break.
"We allowed too many continuations on the defensive end and Howard continued to control the paint on the offensive and defensive ends," Atlanta coach Mike Woodson said. "I played all of our bigs against him to see what we could come up with."
Bibby, the point guard, blamed himself for letting the Magic get the ball in Howard's hands.
"It starts with me," he said. "I need to put more pressure on the ball and make things a little tougher on the point guard."
The Magic improved to 5-1 in the preseason, while the Hawks dropped to 4-3. The teams meet in their regular-season opener at Orlando on Oct. 29.
"All we care about is jelling, because we understand we have new guys on the team," Smith said. "That's all that matters."
Flip Murray scored 14 points for Atlanta. ... Van Gundy said Hedo Turkoglu (right groin strain) may not play until the regular-season opener. ... Orlando's Tony Battie is "50-50 at best" for the final preseason game, the coach added. Battie has a broken left ring finger. ... Each team has one preseason game left. Orlando hosts Memphis on Wednesday, while the Hawks travel to Detroit on Thursday.