Third-seeded Nashville will visit the second-seeded Philadelphia Union in a conference semifinal on Sunday.
With the game tied 1-1 in the 74th minute, Mukhtar, who tied for fifth in the league with 16 goals, dribbled 30 yards to the middle of the penalty area with four defenders in pursuit, then struck a low ball past goalie Pedro Gallese.
Jhonder Cadiz scored in the fourth minute of second-half stoppage time for the final margin.
Daryl Dike put Orlando ahead in the 14th minute before Mukhtar tied it 1-1 in the 21st.
That the match was tight through 45 minutes was expected considering all three meetings this season were draws and Nashville equaled a league record with 18 ties.
It was no surprise that Orlando took the lead on Dike's header off a corner kick by Mauricio Pereyra. Dike took a step back from his defender and flicked a shot from 6 yards past goalie Joe Willis, who tied for the MLS shutout lead with 13.
Nashville conceded the first goal in eight of 17 home games but managed to become the seventh team in MLS history to have an unbeaten home regular season (8-0-9).
There was no shock either that Nashville faced an early deficit as Dike's goal marked the fifth straight match it allowed a goal in the opening 20 minutes.
Mukhtar took a long shot that deflected off Orlando defender Antonio Carlos, causing the ball to sail over Gallese.