The 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
The 23-year-old picked up the problem back in August and was initially expected to be out for just a matter of weeks.
However, he has made slow progress in his recovery from the problem and will now focus his efforts on being ready 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."
Gundogan has been the subject of persistent transfer speculation, with his contract set to expire in the summer of 2015.
Manchester United and Real Madrid are reported to be among several interested parties and Dortmund CEO Hans-Joachim Watzke wants a decision on his future by the end of April.
He told WAZ: "I have the impression that all parties are now aware of the fact that this month a decision must be made. Let's see how it will be."