The tweet was sent a few hours after Daley's disappointing fourth-placed finish in yesterday's 10m synchronised diving competition, from 28-year-old Thomas's Twitter account.
The tweet said: "If there is any consolation for finishing fourth at least Daley and Waterfield can go and bum each other #teamHIV."
Port Talbot have said that they have spoken to Thomas and are satisfied that the tweet was not sent by the player, suggesting instead that he was the victim of a prank after leaving his phone unattended.
"Having spoken at length to the player in question, we believe that he regrettably left his phone unattended and was the victim of a very misguided 'prank'," Port Talbot said in a statement.
"The player issued an immediate apology for the comments which appeared on his Twitter feed and has since deleted his account."
Daley was also the victim of abuse from another Twitter user.