Fernandes had indicated that he would be leaving Sporting after a group of supporters attacked players at the training ground towards the end of last season.
That allegedly resulted in interest from both Newcastle United and West Ham United, but the Portugal international has now opted to remain with Sporting.
At a press conference, Fernandes said: "It doesn't matter who is to blame, now it is over. Sporting is opening a new page and I believe it will be very good."
Fernandes is said to have signed a deal until 2023 with a release clause set at €100m (£88.27m).