The Bucks leapfrogged Miami for sixth in the Eastern Conference. The Heat lost to Oklahoma City on Monday.
Milwaukee won its second straight game without Giannis Antetokounmpo, who is resting a sore right ankle. Both victories came against 50-loss teams.
Nikola Vucevic led Orlando with 17 points and 10 rebounds, while Bismark Biyombo had 14 points.
Bledsoe had 20 points, 12 rebounds and 11 assists for Milwaukee.
But it was Muhammad and Jason Terry who helped ignite the Bucks off the bench during a 20-6 run over the final 5:27 of the third. They helped turn a seven-point deficit into a 74-67 lead going into the fourth.
Terry, the savvy veteran guard, immediately gave the Bucks a spark by forcing a turnover on the inbounds play after Bledsoe's two foul shots. Muhammad gave the Bucks a presence off the dribble to help make up for the absence of the free-wheeling Antetokounmpo.
The Bucks led comfortably the rest of the way to close out the regular season at the Bradley Center. A new arena is scheduled to open in the fall on an adjacent lot in downtown Milwaukee.
The Magic fell to 24-57 but had reason to be confident after beating the Bucks 126-117 in their last meeting on March 14. Orlando was 18 of 34 from 3-point range that night to withstand a 38-point outburst by Antetokounmpo.
The shooting touch was missing Monday, when Orlando was just 5 of 24 from behind the arc.
A game that had the feel of a Milwaukee blowout turned tight after a cold-shooting second quarter for the Bucks. They missed their first 12 shots in the period, with a Bledsoe-to-Khris Middleton layup finally ending the scoreless streak with 5:07 left.
The pace picked up again once facilitators Bledsoe and Middleton (18 points) re-entered the game, with Milwaukee taking a 45-42 lead at halftime.