Walker, who missed the previous two games, was the spark plug all night for the Hornets and became the first player in franchise history with 200 career 20-point games. He made all 14 free throw attempts.
Howard had 12 points and nine rebounds, moving past former Charlotte coach Paul Silas and Dikembe Mutombo for 19th on the all-time NBA rebounding list.
The Hornets raced to a 54-45 lead at halftime behind 13 points from Walker and 11 from Frank Kaminsky, but the Magic trimmed an 11-point deficit to one to start the fourth quarter.
The game turned early in the fourth when Marreese Speights lost his cool.
Speights received a flagrant foul when he shoved Cody Zeller to the ground following a dunk by Kaminsky, giving the Hornets two foul shots and the ball. Zeller made both and Jeremy Lamb was fouled on the ensuing possession, essentially resulting in a six-point swing that allowed the Hornets to take a 86-76 lead.
Walker made sure the Hornets didn't fall apart down the stretch.
He went 1-on-4 on one transition opportunity, but still found his way to the basket for a layup while drawing a foul.
The Hornets were coached by assistant Stephen Silas after head coach Steve Clifford came down with an illness.
"I spent a lot more time delving into the stats, delving into our last game, and really making sure I'm prepared for situations - late-game situations - that sort of thing," Silas said before the game. "It was a long day."
Magic: Only attempted 14 free throws, the same number as Walker. ... Had 20 turnovers that led to 29 Hornets points. ... Were outrebounded 52-40.
Hornets: Only shot 3 of 17 from 3-point range. ... Kaminsky had 14 points off the bench. ... Michael Kidd-Gilchrist had 11 points and eight rebounds.
Magic: Host the Atlanta Hawks on Wednesday night.
Hornets: Host the Golden State Warriors on Wednesday night.
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