The Jamaica Athletics Administrative Association said after last month's national trials that Morgan did not warrant an automatic spot on the team as he came fourth in the competition.
The Court of Arbitration for Sport (CAS) panel sided with the JAAA and concluded the application filed by Morgan was inadmissible.
"I made it clear from the beginning I have no beef with my athletic association, I maintain that I met the necessaries of qualifying and competing at the trials to compete in Rio and be on Team Jamaica," Morgan told Reuters by text message after losing the appeal.
"I believe in the rule of law and l will respect the decision of CAS."
The Jamaican record holder added: "This episode has only made me stronger. I'm now determined more than ever to be in London next year for the world championships."
(Reporting by Kayon Raynor; Editing by Alison Williams)
