The Heat trailed by one point entering the fourth quarter, but Miami outscored Philadelphia 35-25 to secure its sixth win in the last seven home games.
Dwyane Wade had 16 points and Josh Richardson had 13 for the Heat, who moved a half-game in front of Milwaukee and into seventh in the Eastern Conference's playoff race.
Dario Saric scored 20 and J.J. Redick added 18 for Philadelphia.
Embiid, the Sixers' top scorer at over 23 points per game, recorded 17 points but shot just 5-of-18 from the field.
Miami's defense held Philadelphia to just 39.5 percent shooting from the floor.
The final of four meetings started off with the Heat going on a 7-2 run in the first three minutes, led by the three-point shooting of Richardson and inside play of Whiteside.
However, Saric provided a spark, putting the 76ers back in the game and leaving them down 29-28 after the first quarter of play.
Miami scored nine straight points and went on a 12-2 run in the first half of the second quarter to take a 41-31 lead, the first of a pair of 10-point leads and one of 12.
Redick's hot shooting, hitting all three of his three-point attempts, moved Philadelphia to within four at 53-49 at the half.
Three-point shooting and rebounding proved key in the opening half.
Miami was 8-of-14 while the 76ers were 6-of-10. The Heat also outrebounded Philadelphia -- the NBA's top team on the boards -- 28 to 23.
The Sixers were able to build a 67-62 lead with 5:07 left in the third quarter on a 3pointer by Marco Belinelli. Philadelphia held on to lead 74-73 as the quarter ended after Miami went on an 11-7 run.
Embiid went to the bench with his fifth foul with 8:03 left in the fourth quarter.
Miami went on a 10-1 run to take an 88-78 lead with six minutes left.
--Field Level Media
Philadelphia | Miami | |
Dario Saric 20 | Scoring | Hassan Whiteside 26 |
Ben Simmons 8 | Assists | Goran Dragic 7 |
Dario Saric 10 | Rebounds | Hassan Whiteside 8 |
Dario Saric 6 | Free Throws Made | Hassan Whiteside 8 |
Robert Covington 4 | Steals | Goran Dragic 3 |
Ben Simmons 2 | Blocks | James Johnson 2 |
Team | Points | FG% | 3PM-3PA | FTM-FTA | Assists | Rebounds | Blocks | Steals | Turnovers |
Philadelphia | 99 | 39.5 | 15-37 | 16-21 | 28 | 46 | 4 | 9 | 18 |
Miami | 108 | 47.2 | 14-26 | 10-18 | 26 | 49 | 8 | 10 | 16 |