The defeat, in a match between two teams long out of the MLS championship running, was just a footnote on a celebratory night that began with Messi offering his thanks to fans for the welcome he'd received in Florida.
Fans, many of them shouting "Messi! Messi!" in unison, nearly filled the DRV PNK stadium - despite the fact that the club's MLS season ended last month.
"Thank you for being here, for this beautiful tribute," Messi said after raising the trophy he'd collected in Paris last month.
"I have been here for a short time, but it seems like a lot of time.
"I want to thank all the people of Miami, not only those who are here, but in the city in general, for the treatment I and my family have received during this time.
"They showed me a lot of affection, they made me feel at home."
The superstar received a rapturous welcome when he arrived at Inter Miami in July and powered the struggling franchise to the Leagues Cup title in a tournament with MLS and Mexican league clubs in August.
He played his first MLS regular season match for Miami on August 26th as a second-half substitute, scoring a goal in Inter's 2-0 win at New York Red Bulls to snap an 11-match winless streak.
But nagged by a late-season leg injury, Messi was unable to lift Miami from the league cellar into the MLS Cup playoffs.
Even so, he has electrified the US league, his appeal underscored by a spike in jersey sales and a rise in sales of MLS season pass viewing subscriptions as well as ticket sales wherever Miami played.
Fans were chanting for him again late in Friday's match, but he was unable to produce an equalizer in a contest won by NYCFC with goals from Talles Magno and Julian Fernandez.
Messi's latest Ballon d'Or rewarded exploits achieved well before his move to MLS, namely his inspirational performances at last year's World Cup in Qatar where he scored seven goals and was named the tournament's best player as he carried Argentina to victory.
But Messi said he was aiming to build on Miami's Leagues Cup crown next season - when his club will defend that title and compete in the US Open Cup and CONCACAF Champions Cup in addition to their MLS campaign.
"I had no doubt that we were going to have a good time, that we were going to enjoy ourselves and today I have even less doubts that next year is going to be much better," he said.
