Mickelson's victory put him in such a solid position in the season-ending point standings that only four players can pass him during this week's BMW Championship, which begins Thursday in Illinois.
He told NBC Sports that he and PGA Commissioner Tim Finchem had had talks about a "couple of things" Mickelson said he wanted done if the golfer was to guarantee to appear in the four FedEx Cup events. Those weren't done, Mickelson said without detailing his requests.
"This decision was not an easy one to make," Mickelson said in a statement, "and in no way is meant as disrespectful to the tour or 'sending a message' to anyone. I've talked for weeks about needing to find a balance between my game, my business affairs and my family and now is the time for me to take some time off."
He said he would play the Tour Championship in two weeks.