Leonardo resigned from his position on Wednesday following the announcement that he will be banned for 13 months for pushing a referee last season.
"I really understand his decision," Al-Khelaifi told L'Equipe. "I respect it, even if I regret it deeply.
"Leo has done an excellent job over the past two years to bring a lot of credibility to the sporting aspect of our project. I thank him for this work and wish him the best for the future.
Al-Khelaifi also said that the club would still be able to achieve their ambitions without Leonardo.