The Borussia Dortmund midfielder suffered a back injury in August and, though his condition continues to improve, he will not be ready in time for the tournament in Brazil
Gundogan's future at Dortmund is under speculation, with Manchester United considering the midfielder one of their top summer transfer targets along with Bayern Munich star Toni Kroos.
Gundogan picked up the problem back in August and was initially expected to be out for just a matter of weeks, but will now focus on being fit for pre-season.
"Ilkay will not play at the World Cup," said Klopp.
"It is very hard for him to deal with. His back is better, it is all good, but it takes time to recover completely. We just have to wait."