Atletico’s president Enrique Cerezo had claimed that the club could not afford the fee, believed to be above €10 million, required in order for the on-loan goalkeeper to feature against his parent side.
But after the two sides were paired together in Friday's draw, Uefa stated any clause in the 21-year-old's contract with Chelsea is “null, void and unenforceable” during a Champions League fixtue.
A statement from Uefa read: “The integrity of sporting competition is a fundamental principle for UEFA.
“Both the UEFA Champions League and the UEFA Disciplinary Regulations contain clear provisions which strictly forbid any club to exert, or attempt to exert, any influence whatsoever over the players that another club may (or may not) field in a match.
“It follows that any provision in a private contract between clubs which might function in such a way as to influence who a club fields in a match is null, void and unenforceable so far as UEFA is concerned.
“Furthermore, any attempt to enforce such a provision would be a clear violation of both the UEFA Champions League and the UEFA Disciplinary Regulations and would therefore be sanctioned accordingly.”
Chelsea chief executive Ron Gourlay was quizzed over the news after Friday's semi-final draw and said the Blues had no issue with Uefa's ruling.
He said: "The loan was arranged at start of the season, it's simple, Thibaut can play against Chelsea, that was never in doubt.
"We'll evaluate the Uefa statement over the next 24 hours, we've complied with the loan rules. Thibaut can play against Chelsea in both ties if selected by Atletico."