It was only her second competitive appearance since winning gold at London 2012 and she finished fourth in the 100m hurdles and eighth out of eight 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 win in Moscow," she said. "The time has now come to stop chasing fitness and look to cure the problem."
Coach Toni Minichiello explained there had not been enough improvement in the athlete's condition to ensure she could complete both days of the heptathlon event in Moscow.
"There are nine global medals up for grabs over the next three years not including Moscow," he said. "So a long term view has been taken."
Minichiello added that while Ennis-Hill was disappointed to be missing the World Championships, she was also relieved to be able to move on.
"Up until this point it was maybe she can go, maybe not, and it is difficult to be on the edge like that," he added.
Toni Minichiello on Ennis-Hill injury
"Yes it is not the best decision because it is a negative, but a decision has been made and I think as a sportsperson you get a lot of solace from that because the line in the sand has been drawn and you can step forward and move on from it."
Neil Black, UK Athletics performance director, said: "No-one wants to see her competing in pain. We look forward to seeing her wear the Great Britain and Northern Ireland vest again in 2014."
Ennis-Hill's withdrawal from the Great Britain squad means the remaining track and field athletes who won gold at London 2012 are long-distance runner Mo Farah and long jumper Greg Rutherford, who was himself selected
despite fitness concerns.
UK Athletics said there would be no replacement for Ennis in the squad as none of the potential candidates had reached the required 'A' qualifying standard.
That leaves Katarina Johnson-Thompson, 20, as Britain's sole entrant.
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