Varane admitted full responsibility for his mistakes in a series of post-match interviews, but Kroos stopped short of placing the blame on the France international.
"We didn't play a good first half and helped them with the goals," Kroos told reporters.
"After that, it will, of course, be difficult to turn the game around.
"Rapha played an outstanding season. There are no accusations."
Kroos has also insisted that he is now fully focused on taking a short break before the next season begins - and has no plans to watch the rest of the competition unfold.
He added: "I want to win every title that is possible. So at the moment, I'm disappointed. Then I'm looking forward to a holiday. I probably won't watch the rest of the competition."