The Ligue 1 champion's president has made it clear the Uruguayan was always the club's No.1 target this summer and has rubbished suggestions Zlatan Ibrahimovic could leave.
Cavani completed the 64 million euro signing of the Uruguay star on Tuesday after weeks of speculation over the forward's future, during which time Rooney was also linked with the French champion.
However, Al-Khelaifi has clarified that Cavani was always the No.1 choice for Laurent Blanc's side, and insisted the 26-year-old was not motivated to make the move by money.
When asked whether Rooney or Cavani had been the top target, Al-Khelaifi told Le Parisien: "Of course Cavani was our first choice, the coach's, Leonardo's and mine. He really wanted to come to Paris, although other big clubs wanted him. If he had not believed in the project, he would not have come.
"Cavani did not chose Paris for the money, believe me 100 percent. He believes in the project, he believes that, with us, he will be able to win many titles."
Speculation has been rife that Cavani's arrival could signal the end of Zlatan Ibrahimovic's career in Paris, with the Sweden star having been linked with a return to Juventus in recent weeks, as well as the likes of Manchester City.
Al-Khelaifi, however, will not entertain the notion of letting last season's talisman leave.
"Ibra will stay, that's for sure. He'll play with Cavani."