Griffin Dorsey and an Amine Bassi penalty put Houston 2-0 up in Fort Lauderdale, Florida.

Josef Martinez scored a consolation for Miami in stoppage time.

Houston goalkeeper Andrew Tarbell made three saves as Dynamo clinched their second US Open Cup in five years.

Miami's Spain defender Jordi Alba also missed the game because of injury.

Miami manager Gerardo Martino said Argentina World Cup winner Messi's return to full fitness was the club's top priority.

"It was not prudent for him to play. We couldn't even consider playing him for a few minutes because we would be taking risks," said former Barcelona and Argentina boss Martino.

Martino said Messi will "certainly play before the league is over".

The regular MLS season ends on 21 October, with the play-offs taking place from 25 October to 9 December.

Messi has scored 11 goals and provided five assists for the MLS franchise since joining in July after his Paris St-Germain contract expired.