Courtois is in his third season on loan with the Spanish club from Chelsea and the teams were paired together in Friday's draw in Nyon.
Media reports suggested Chelsea and Atletico agreed a clause in the keeper's contract that the Madrid team would pay around £5m in compensation if the clubs clashed in European competition.
And Atletico have indicated that they would not be prepared to field him at that price, and would abide by the agreement with the Blues.
UEFA became involved on Friday morning, insisting that they would overrule any attempt by Chelsea to bar Courtois from playing.
Sky Sports' Spanish football expert Guillem Balague says Chelsea and Atletico may have cut a deal which would see Courtois sit out the Champions League double-header, in return for the Blues agreeing to the keeper returning to Madrid next season on loan.
Gourlay insists there is no question of the Blues standing in the way of the Belgium international playing in the semi-finals - though he made no mention of any fee the Spaniards would have to pay.
"The loan was arranged back at the start of the season," he told Sky Sports News. "It's quite simple - Thibaut can play against Chelsea. That was never in doubt. Regarding the UEFA statement, we'll evaluate that in due course. As far as Chelsea's concerned, we've complied with the loan rules."
A UEFA statement issued prior to the draw read: "In response to media reports referring to the situation of Club Atletico de Madrid goalkeeper Thibaut Courtois, UEFA would like to reiterate its position.
"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."