The London 2012 Olympics champion withdrew from the championships starting in the British capital next week due to an ankle injury.
“I gave it everything and this time fell short I won’t be at the London 2017 World Championships to defend my title,” Rutherford said in a social media post.
“The ankle injury and herniations just haven’t healed and I’m totally unable to jump/sprint, or even cough for that matter, without pain.
“Wishing the amazing British team all the luck in the world. I know how it feels to succeed in that stadium. It’s the greatest feeling in the world.”
The Briton would have been one of Manyonga’s greatest threats in his pursuit of his maiden senior world title.
Rutherford won the 2012 Olympic title in front of his home crowd and followed that victory up with the world title in Beijing in 2015 before finishing third behind Manyonga at last year's Rio Olympics.
Manyonga is the overwhelming favourite to win the long jump title in London with fellow South African Ruswahl Samaai also in with a good chance.
The SA duo dominate the 2017 world rankings with Manyonga boasting the four best jumps this year.
His national record of 8.65 metres is at the top of the pile while he also has three more jumps of over 8.60m to highlight his dominance.
Samaai goes into the championships as the second best jumper of the year with his personal best of 8.49m.