Facundo Farias, Jordi Alba and Leonardo Campana scored to cancel out Ryan Hollingshead’s effort for the hosts.
The statement victory against last season’s MLS Cup winners puts Miami nine points shy of the play-offs with nine games to play.
Since Messi, 36, made his debut on 22 July, Inter Miami have won the Leagues Cup and are unbeaten in 11 fixtures.
The Argentine World Cup winner has scored 11 goals and chipped in with five assists in 11 appearances across all competitions.
Inter Miami return to the DRV PNK Stadium in Fort Lauderdale for their next match against Sporting Kansas City on 10 September.
Messi is regarded as football royalty and he was watched by British royalty with Prince Harry taking up the opportunity to see the former Barcelona and Paris St-Germain forward in the flesh.
Actors Leonardo DiCaprio, Will Ferrell, Tom Holland, Toby Maguire, Owen Wilson and Gerard Butler were also named on the ‘notable attendees list’, while musicians Liam Gallagher, Selena Gomez, Tyga, BReal and Nas also packed in to the 22,000-seater stadium.
