The 26-year-old American had led the FedEx Cup standings following his first win on the PGA Tour last weekend.
Zalatoris won the FedEx St Jude Championship in Memphis after three times finishing second in majors - at the Masters in 2021 and the US PGA Championship and US Open this year.
The official PGA Tour Twitter account posted footage of Zalatoris having treatment on the course for his injury, but he was forced to withdraw during Saturday's third round at Wilmington Country Club.
The season-ending Tour Championship starts at Atlanta's East Lake Golf Club on Thursday.
Zalatoris' manager Allen Hobbs said in a statement: "Will tweaked his lower back during a shot on the third hole today.
"After getting it worked on and the pain not subsiding, he felt that it was best to withdraw from the BMW Championship so he can work with his trainer the next few days to get the inflammation to calm down.
"Will looks forward to playing next week in Atlanta."
Adam Scott headed into the third round of the BMW Championship as the leader on eight under par.
Scott held a one-shot lead over world number one Scottie Scheffler, Jordan Spieth, Cameron Young and Corey Conners, with Northern Ireland's Rory McIlroy part of a five-man group on six under.
Zalatoris had been five shots behind Scott at the halfway stage.