The Qatari businessman assured that his sporting director will not be leaving and declared himself pleased with his club's qualification for next season's Champions League
Carlo Ancelotti's side narrowly lost out on the Ligue 1 crown to Montpellier, and relations between the PSG supremo and the Brazilian were reported to have gone sour over the club's transfer strategy and general quality of play.
But Al-Khelaifi told AFP news agency: "I will not answer the rumours but I can confirm that Leonardo will stay.
"He has done an excellent job this season and has excellent relationships with everybody here in Qatar."
Despite missing out on the league title, Al-Khelaifi said he was pleased with the club's progress on and off the pitch this season.
"I am disappointed not to win the title, but very happy to have met the target that was the Champions League," he said.
"We must commend the president of Montpellier, his team and staff. They deserve it.
"[But] what I can promise fans is that the future belongs to PSG."
The 38-year-old also said he was considering demolishing the club's iconic Parc des Princes stadium to build a new 60,000-seater in its place.
"Paris is the capital. The city deserves a bigger stadium," he explained.
"Attendances have increased a lot this season and they'll increase even more next season in the Champions League."
PSG finished second in the Ligue 1 table, three points behind champions Montpellier.