As their thrilling US Open Cup semifinal ended 3-3 after extra time in Ohio, Inter Miami advanced into another final after rallying from a 2-0 deficit to defeat Cincinnati on penalties.
Miami is currently one victory away from winning their second championship since Messi joined the team last month after defeating Nashville on penalties to win the Leagues Cup on Saturday.
The US Open Cup, which has been played since 1914 and is comparable to the FA Cup in England and the Copa del Rey in Spain, is the oldest and most significant knockout tournament in American soccer.
Houston Dynamo will play Miami in the championship match on September 27 after the Texans defeated Real Salt Lake 3-1 in overtime.
Cincinnati, who is currently leading Major League Soccer while Miami is at the bottom of the standings, would have been the clear favorite a month ago. However, the Florida team is now a significantly different squad from the one that had lost all 11 of its league games prior to the Argentine's arrival.
Miami's streak of victories since bringing in Messi and the Spanish duo of Sergio Busquets and Jordi Alba appeared to be coming to an end in the sweltering heat with temperatures over 100 degrees fahrenheit (38 Celsius) at kickoff.
With 22 minutes left in the game, Inter was behind 2-0 when the Argentine gave Leonardo Campana two flawless assists that forced overtime.
Luciano Acosta, a fellow countryman of Messi, gave Cincinnati the lead in the 18th minute, and American striker Brandon Vazquez doubled Cincinnati's advantage in the 53rd minute with a powerful shot from the edge of the box.
Messi's left-footed free-kick from the 68th minute was headed in by Campana to give Gerardo Martino's team some life after they had put in a sluggish performance up to that point.
Yuga Kubo's attempt, which Cincinnati believed had made it 3-1, was disallowed due to handball.
When Campana received a pass from Messi at the back post in the seventh minute of stoppage time, the Ecuadorian attacker once more found the back of the net to force overtime.
Josef Martinez scored Miami's opening goal of the game with a perfectly executed finish after Benjamin Cremaschi produced an amazing ball into his path.
However, Cincinnati came back in the second period with to a right-footed shot by Japanese winger Kubo that went past a leaping Drake Callender and into the far corner.
When Nick Hagglund's penalty for Cincinnati was stopped by Callender in the shootout's 4-4 tie, Cremaschi made the subsequent attempt to guarantee Miami's spot in the championship game.
After Cremaschi's game-winning penalty kick, Messi congratulated the Argentine-born 18-year-old from Miami.
"I'm living a huge dream," he stated to CBS Sports. "Sometimes I sit down and really think about the position that I'm in and it's incredible, I never believed I was going to be in the spot that I am in now," he added.
Martino, whose team must now begin its 12-game bid to move up from last in the Eastern Conference to the playoff spots, offered a more sober perspective.
After a demanding eight-game stretch, Martino said he could be obliged to rest some of his players, including Messi.
Leo and many other players are "reaching a critical physical limit," he said. "Starting today, we will evaluate how we approach the next three matches."
"All the enthusiasm overcomes the exhaustion... I wish the team could perform better in the future, but it's really challenging to achieve that when you practically never get to sleep.
Hector Herrera, a Mexican international, gave Houston the lead just before halftime, but Salt Lake tied the score in the 64th minute with a goal by Julio Anderson.
Adalberto Carrasquilla, a Panamanian midfielder, scored a spectacular solo goal in extra time, and Luis Caicedo sealed the victory late.
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