Villeneuve's exit was expected since the club's board of directors resigned last Sunday and called for an extraordinary meeting, now set for February 3.
"Charles Villeneuve will resign as club president on February 3, prior to the general assembly to be held the same day," PSG said in a statement on their website.
The board members had said in a statement this week they could "no longer serenely fulfil their duty alongside a president they can no longer trust".
The conflict was sparked by a letter sent by Villeneuve to the board members in which he said there were issues at the club and asked for more power. The club is owned by U.S. property company Colony Capital.
Former journalist Villeneuve, 67, was named PSG president last May. The Paris club, who narrowly escaped relegation last season, are sixth in the Ligue 1 standings, six points behind leaders Olympique Lyon.
