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, the British star finished a disappointing fourth in the 100-meter hurdles and eighth in the long jump.
"Up until now we have been focusing on managing the pain so I can train and get myself in shape to go out there to win in Moscow — which has meant not focusing on finding a cure for the injury," Ennis-Hill said in a statement. "The time has now come to stop chasing fitness and look to cure the problem.
"I am so glad I got to compete in London last weekend as it gave me a clear picture of where I am - and it is definitely not where I want to be both regarding pain and also form. To say I am gutted is an understatement — no athlete likes to miss the opportunity to compete at a major Championships — they don't come round that often."
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 Chernova has also withdrawn with an injury.
"It's not been the easiest or simplest of decisions," coach Toni Minichiello said. "The pain management did improve, and Jessica was able to compete in London, but the next few days have not seen enough improvement that would have made completing the two-day, seven events of the heptathlon possible.
"I've also had to consider if competing at the world championships would cause further damage, making any rehab more difficult. There are nine global medals up for grabs over the next three years not including Moscow. So a long term view has been taken."
It is the latest blow to the world championships, which are already without Jamaican sprinters Asafa Powell and Sherone Simpson, as well as American Tyson Gay, after they all failed doping tests in recent weeks.
Defending world 100-meter champion Yohan Blake has also pulled out with injury as has Olympic 800 champion and world record-holder David Rudisha.