Major League Soccer's refereeing body replaced the match official for Inter Miami's home game with Orlando City on Saturday after pictures of him in a Miami jersey appeared online.
Referee Guiherme Ceretta was replaced by Jaime Herrera for the fixture by the Professional Referees Organization (PRO).
A spokesman for PRO confirmed to ESPN that "Referee Guiherme Ceretta was removed from the game due to a potential conflict."
The Miami jersey has become the biggest selling shirt in MLS after Lionel Messi joined the club in July.
Messi was in the starting lineup for Saturday's Florida derby against Orlando.
MLS's regular referees are currently locked out by PRO after talks broke down over a new collective contract.
The Professional Soccer Referees Association (PSRA) rejected an offer from PRO and the league began last month with replacement referees from outside the PSRA's ranks.
