The problem has been bugging the 23-year-old since April and forced him to miss June's Jamaican Trials event.
Blake had already qualified for August's championships in Moscow as the defending 100m champion, but will now be denied the chance to retain his crown.
"This decision was made after continual assessment and re-evaluations since his withdrawal from the Jamaican Senior Championships," his manager Cubie Seegobin told Reuters.
"Yohan has made vast improvement, although the injury sustained in April of this year has prevented him from attaining the necessary fitness levels that we have grown accustomed to seeing in his competition performances."
Blake won the 2011 title in Daegu when compatriot Usain Bolt false-started.