The Italian left back hurt himself during the 1-0 win against Bolton last Sunday.
Everton boss David Moyes said: "Pistone has a cruciate injury and looks like he will be out for most of the season. It is a massive blow and I will probably need to bring in a left-back."
The development is expected to make Everton rush through a deal to bring fellow Italian Matteo Ferrari in as cover for the player.