Messi, making his 115th appearance for the Miami, struck 24 minutes into the annual match between the MLS Cup holders and the Mexican Campeon de Campeones winners. Casemiro scored a late goal to secure the win.
Former Barcelona and Paris Saint-Germain forward Messi joined Miami in 2023 and has helped them win four trophies so far.
The 39-year-old, who is Argentina's all-time highest scorer with 125 goals and led them to a World Cup triumph in 2022, announced his retirement from international football last month and will take his final bow for the national team in a friendly against Benin on October 6.