Ruiz clinched a £10.6million switch from tonight's opponents Twente to Craven Cottage on transfer deadline day under the impression that he could still play in Europe this season.
But the striker's appearance in the Dutch club's losing Champions League qualifier last month means he is cup-tied.
Jol admitted: "If he'd known before it maybe could have been a problem. I don't agree with this rule. I'd like all my players to be available. Maybe if they were playing in the same competition it would be OK , but this is a different competition."