Nakayama was named in Japan's 26-man squad for Qatar on Tuesday and was expected to start in their Group E games against Germany, Costa Rica and Spain.
Huddersfield said the 25-year-old will require surgery that will rule him out for the rest of the Championship season after being stretchered off in the Terriers' 2-0 home defeat to Sunderland on Wednesday.
Japan manager Hajime Moriyasu had yet to name a replacement in his World Cup squad as of Friday morning. The tournament starts on November 20.
Huddersfield head coach Mark Fotheringham said Nakayama's injury was "a huge blow" for the side that sit bottom of England's second tier.
"On a personal note, we are all devastated that Yuta will be unable to join up with Japan for the 2022 FIFA World Cup, which is an experience he had completely earned."
Nakayama's absence means 36-year-old former Inter Milan full-back Yuto Nagatomo will likely start for Japan in what will be his fourth World Cup.
Japan launch their campaign against Germany on November 23, before taking on Costa Rica on November 27 and Spain on December 1.
