Uefa released a statement shortly before the draw in Nyon on Friday morning, which paired the two sides, stating that any clause in Courtois' contract would be “null, void and unenforceable” in European competition.
The governing body's general secretary, Gianni Infantino, also warned that the Londoners would face sanctions if they planned to fight the ruling, but club chief executive Ron Gourlay has insisted that there will be no issue.
"The loan was arranged back at the start of the season and it's quite simple: Thibaut can play against Chelsea, that was never in doubt," he told Sky Sports.
"Regarding the Uefa statement that came out, we'll evaluate that in due course over the next 24-48 hours.
"But as far as Chelsea's concerned we've complied with loan rules. As far as the player concerned, he can play against Chelsea, if selected by them of course."
The first leg of the semi-finals will be held at the Vicente Calderon, with Stamford Bridge hosting the decisive return leg.