The 26-year-old has been suffering from back problems since December and has not played since then.
The center-back has tried to play his way back after the injury, but was ultimately forced to undergo surgery.
"I am of course disappointed that I will miss the World Cup," de Ligt writes on Instagram.
The Netherlands will begin the tournament's group stage against Japan on June 14. After that, Sweden awaits on Midsummer's Day on June 20 and then Tunisia on June 26.
The Netherlands have postponed their squad selection. The World Cup squad was due to be presented on May 25 but has been moved to May 27.
