"After careful consideration, I have decided to leave Saracens at the end of the current season," said Jones, who was part of South Africa's World Cup winning coaching team in 2007.
"My reasons are entirely personal. My wife and daughter have always given me unqualified support but it is now time for me to put the family needs first.
"I have greatly enjoyed my time with Saracens extending back to 2006 (when he worked with the club as a consultant) and I wish the directors, staff and players well in the future.
"Naturally I remain 100% committed to the Saracens cause and eagerly look forward to building on the progress we have made this season and ensuring we challenge for a top-four finish in the Premiership and maintain our strong momentum in the European Challenge Cup."
Jones, who took over from Alan Gafney after the Irishman moved to Leinster last summer, will be replaced by former South African centre Brendan Venter.
Venter coached London Irish to the Powergen Cup back in 2002 and is currently an assistant coach with South African Super 14 franchise the Stormers. He won 17 caps for the Springboks between 1994 and 1999 and is highly thought of in his home country.
"Brendan has an outstanding knowledge of the Guinness Premiership, following his success as coach at London Irish, and he has become well known and well respected at Saracens during the course of this season, after being introduced and recommended by Eddie as a specialist coach," said Saracens' chairman Nigel Wray.
"We warmly welcome him to the club on a full-time basis."
Venter's appointment heightens the South African connection at Saracens, who have received substantial investment from a South African company and are rumoured to be looking into a possible move to Fulham, an area of London highly-populated by South Africans.
Such a move would enable Sarries to tap into the support of some 750,000 South Africans living in the area, especially as rumours continue to crop up about the possible signing of Springbok flanker Schalk Burger on a short-term contract next season.