The 30-year-old had been battling to be fit in time for next month's competition at the Olympic Stadium in London, where he won Olympic gold for Great Britain in 2012.
Rutherford says that he did all that he possibly could to make himself available for the Championships, but after a number of setbacks he has admitted defeat in his bid to take part.
"With an incredible start to the year in training, and very promising early season form, I have had a difficult series of setbacks as the season progressed," he said in a statement.
"Most recently, a badly damaged ankle ligament and a sportsman's hernia, really put paid to my plans. The injuries have taken longer to heal than we hoped, and I have been unable to even jump at all in training, let alone compete.
"I am truly gutted. That stadium is such a special place for me, I am so devastated that I won't be competing in front of the best fans in the world, in the stadium that changed my life. My focus will now turn to 2018 and becoming a three time European champion on the trot, something no long jumper has ever done before."
Fellow British athlete Richard Kilty has withdrawn from the 4x100m relay, meanwhile, due to a broken finger.