The 39-year-old Argentine opened the scoring in the 24th minute, rising to head home a cross from longtime teammate Luis Suárez.
Casemiro added a second goal in the 81st minute, heading in a corner delivered by Messi to seal the win.
The Brazilian midfielder has scored four goals, all headers, in his last five matches after scoring in three consecutive games against CF Montreal, Atlanta United and Chicago.
The victory gave Inter Miami another trophy three years after Messi’s arrival.
Miami won the Leagues Cup in 2023, the Supporters’ Shield in 2024 and MLS Cup in 2025.