Ennis-Hill has been struggling with an Achilles injury but returned to compete in the Anniversary Games at London's Olympic Stadium over the weekend.
However, she finished a disappointing fourth in the 100m hurdles and eighth in the long jump.
On Wednesday, Ennis-Hill says she is "not where I want to be both regarding pain and also form" and adds "to say I am gutted is an understatement."
Ennis-Hill made decision with coach Toni Minichiello, who says there were fears that "competing at the world championships would cause further damage, making any rehab more difficult."
The 27-year-old Ennis-Hill was looking to regain the world title she lost to Tatyana Chernova of Russia in 2011. Chernova has also withdrawn with an injury.