Courtois made the social media post on Friday as it became clear Costa would not be re-signing for Atletico.
Some interpreted the message as a swipe at Atleti fans, but Courtois, who spent three seasons with the club, insisted this was not the case.
He told Onda Cero: “I appreciate and I have a lot of respect for Atlético fans. I apologize if I offended some of them. It was only a joke between friends.