Van Nistelrooy was appointed in March last year as a replacement for Roger Schmidt, signing a three-year contract.
But the former Manchester United and Real Madrid striker has opted to leave with one game of the Eredivisie season still remaining.
PSV will finish in second position if they avoid defeat to AZ Alkmaar on Sunday.
Van Nistelrooy won the Dutch Cup and Dutch Super Cup in his only season in charge.
A statement on the club's website read: "Head coach Ruud van Nistelrooy announced on Wednesday morning that he would leave PSV. After several discussions about internal affairs that have taken place in recent weeks, a meeting took place on Tuesday evening between the Board of Directors and Van Nistelrooy. It was decided to keep the focus on next Sunday's match against AZ and to continue talking after the season.
"Van Nistelrooy reported this morning that in his opinion there was not enough support within the club to continue longer. He immediately explained this to the players and staff. This Sunday, at the request of the management, Fred Rutten will temporarily take over his role as Head Coach. PSV regrets Van Nistelrooy's decision and is grateful to him for winning the Johan Cruyff Shield and the TOTO KNVB Beker this season and hopes to close the football year with second place."
The 46-year-old had a spell with PSV as a player, winning two Eredivisie titles before further stints at Manchester United, Real Madrid, Hamburg and Malaga.