Fortune ended last season on loan at the Britannia Stadium and Tony Pulis has been working tirelessly all summer to bring him - and a number of the Potters' other loan stars - back to the club.
Pardew claims he accepted Stoke's bid for the good of the player as he can no longer guarantee him regular action at The Valley.
He told the club's official website: "I'll be honest, we have accepted a bid from Stoke purely for Jon's sake rather than my own.
"I think there is the opportunity for him to play definitely in the first team there, but maybe he is going to stay and continue his career here and hope to get in our first team."
Fortune is thought to be keen on a return to the Potteries but may prefer a loan move as City can not match his current wages.
However, neither club are keen on such an arrangement so the 26-year-old is likely to complete his switch in the next few days.
And he may be joined by a number of other new faces as the Potters close in on some of his other top targets.
Richard Cresswell has already agreed a move from Leeds and Pulis has revealed he hopes to sign "six or seven" more before the season gets underway at Cardiff next weekend.
The Welshman told Stoke City World he is "very close" to strengthening his squad further and hopes to field a number of new signings in Friday night's final pre-season friendly at Tranmere.
Salif Diao is close to putting pen to paper on a two year deal, while Isaiah Osbourne has been linked with a season-long loan.
Pulis did not comment on Osbourne specifically, but did confirm he would talk to Villa boss Martin O'Neill over any players he may have available.