The Argentina forward, 36, had two assists in a thrilling US Open Cup semi-final at FC Cincinnati, which ended 3-3 after extra time.
It was the first time Messi failed to score for Miami, in his eighth game for the club, but he converted his penalty as they won the shootout 5-4 in Ohio.
Miami also beat Nashville on penalties to win the Leagues Cup on Saturday.
That was the club’s first major honour since being formed as an expansion team in 2020.
They will now make their first appearance in the final of the US Open Cup, America’s oldest and most prestigious knockout football competition, which dates back to 1913.
Miami will host the Houston Dynamo on 27 September after they beat Real Salt Lake 3-1 after extra-time.
Cincinnati were top of the MLS standings when the season was paused for the Leagues Cup in July while Miami were bottom.
But Miami are unbeaten in eight games after signing Messi and his former Barcelona team-mates Sergio Busquets and Jordi Alba.
Cincinnati led 2-0 with 22 minutes remaining after goals by Luciano Acosta and Brandon Vazquez before Messi twice crossed for Ecuadorian striker Leonardo Campana to score with headers – the equaliser coming deep into stoppage time.
Josef Martinez put Gerardo Martino’s Miami side in front early in extra time from a Benjamin Cremaschi pass, before Yuya Kubo made it 3-3 on 114 minutes.
With the shootout level at 4-4, Miami goalkeeper Drake Callender saved Nick Hagglund’s penalty before Miami-born Cremaschi, 18, converted the decisive spot-kick.
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