Howard ended with 15 points and nine rebounds for the second-seeded Magic, who won the opener, 98-89, on Sunday. Jameer Nelson and Rashard Lewis each scored 13 and Matt Barnes ended with 11 in the win.
Howard, fresh off being named the NBA's Defensive Player of the Year for a second straight season, picked up three fouls in the first half and had his fourth midway through the third quarter. His fifth foul came with 5 1/2 minutes left, but by that time the defending Eastern Conference champions were in command.
"We have to find a way to get him on the court 38, 39 minutes, particularly on the road in Charlotte," Magic coach Stan Van Gundy said. "It will be tough for us to survive him playing 28 minutes."
Stephen Jackson, playing despite a bruised left knee, had 27 points, but also committed seven of the Bobcats' 21 turnovers. Gerald Wallace contributed 15 points for Charlotte, which failed in an effort to pick up the franchise's first playoff win.
"We have to take better care of the ball," Bobcats coach Larry Brown said. "We have to share the ball much better."
Game 3 of the best-of-seven series is Saturday afternoon in Charlotte.
Ahead 41-30 at the half, the Magic widened the lead with a big third quarter thanks to a 12-of-18 effort from the field. Howard led the way with nine points in the period.
Wallace's layup had the Bobcats within 54-45 with 5:48 left in the third quarter, but the Magic came back with an 11-2 burst and widened the lead to 75-55 going into the final quarter.
Orlando, which went 10-of-27 from three-point range, got two big shots from beyond the arc from Lewis and one from Nelson in the latter stages of the third quarter.
Charlotte had one last push, scoring nine in a row to get within 83-75 with 3:16 left following a Wallace layup.
Carter responded with a jumper, and then the back-breaker came for the Bobcats. Jackson drove into the lane, but lost the ball as Barnes made contact with the Charlotte guard's headband. That left it over the eyes of Jackson, but no foul was called. Nelson broke out the other way for a layup and converted the subsequent three-point play with 1:34 remaining for an insurmountable 88-75 cushion.
"We're waiting until they hit and trying to respond," Jackson said. "It's too late, they're being more of an aggressive team."
It was a horrible start for the Bobcats, who went 5-of-17 in the opening quarter. Orlando raced to a 13-3 lead with under five minutes left in the period. Despite the poor shooting, Charlotte was down only 18-14 after 12 minutes.
The Bobcats, who never led, were behind by double digits a good portion of the second. D.J. Augustin's three-pointer had the visitors within 37-30, but Carter converted a free throw and Ryan Anderson's three-ball in the final minute provided a 41-30 halftime difference.
Howard rocked the rim with a thunderous jam after a power move on Theo Ratliff for a 50-38 lead with 7 1/2 minutes left in the third.
"It's important for us to remain consistent," Carter said. "I think with a team like this, which is very stingy on the defensive end, you don't want to force things. The fortunate thing for us is we have a lot of weapons. We're getting it from a lot of guys. It's a luxury."
The Magic went 24-of-35 from the foul line...Nazr Mohammed had 10 points for Charlotte, which shot 43.9 percent from the field...Including these two playoff games, Orlando has beaten Charlotte in 12 of the last 14 meetings.