Brazil defender Silva, who joined from AC Milan last summer, has been attracting the interest of Spanish giants Barcelona in recent weeks.
Ibrahimovic was also a big-money arrival from Milan in 2012, costing in the region of €20million (£17.2million), but has been linked with a swift return to Serie A.
The Ligue 1 champions are certainly under no financial pressure to sell thanks to the backing of owners the Qatar Investment Authority.
They yet again demonstrated their muscle in the transfer market by completing a reported £55million deal for Napoli striker Edinson Cavani on Tuesday.
Al-Khelaifi says that deal highlights their determination to build a side capable of winning the Champions League and is not entertaining the thought of selling key players.
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."