Messi extended his winning streak since joining the MLS side to seven games.
Inter Miami crushed Philadelphia Union 4-1 to set up a title clash with Nashville SC.
Inter Miami will meet Philadelphia away on Tuesday (Wednesday 4.30 am IST) for a place in the final.
Inter Miami will next face FC Dallas, who beat Mexican side Mazatlan 2-1.
Messi drew a foul about 25 yards from goal in the dying seconds and stepped up to deliver what everyone came to see as his free-kick sailed into the top left corner and sent the crowd into delirium.
A packed stadium greeted the seven-time Ballon d'Or winner during his unveiling in Florida.
Messi is expected to make his debut on Saturday (July 22) when Miami host Mexico's Cruz Azul in their Leagues Cup opener.
The 60-year-old coached Messi and Busquets at Barcelona in 2013-14 before managing Argentina from 2014-16.
The major setback for the fans would be his absence in the Champions League.
The Argentine great, who is a free agent after parting ways with PSG, is expected to join the MLS side.