It had been suggested that Edinson Cavani's move from Napoli would signal the end of Ibrahimovic's career with the capital outfit. Silva, meanwhile, has been widely linked with a move to Barcelona this summer.
However, Al-Khelaifi has reiterated that neither player will be leaving the Ligue 1 champions.
He told L'Equipe: "Will Thiago Silva and Zlatan Ibrahimovic stay? I already told you: Yes. Thiago's agent has been very clear. It is the same for Ibra. The project will go on.
"People talk about our credibility but we have just signed Edinson Cavani, one of the best forwards in the world.
"A lot of clubs wanted him but he signed at PSG. Our objectives remain the same: Win the Champions League within four years."
Real Madrid have been strongly linked with a move for Ibrahimovic in recent weeks.