No, they will definitely be tired. They were tired today and it showed, and it almost cost them the game. The silly foul that led to that free kick and the lack of reaction in the set piece can at least be partly explained because of that. Furthermore, it was obvious they were tired. Some of them even were clearly injured, and others are in danger of injury -- this includes players as important as Modric and Mandzukic, simply because of the minutes played, distances ran, intensity, and rest time. So it will definitely be a factor.
Having said that, of course they still have a chance.
England would still be favorites even regardless of the physical aspect. IMO Croatia should be playing better, more free flowing football with that magnificent squad. I'd think especially for this game and given the circumstances the formation should switch to a three men midfield with Modric and Rakitic better covered, freer to create, covering less ground, and having to do less defensive duties.
"It is possible to imagine a distant future in which most other species of life are extinct but the ocean will consist overwhelmingly of immortal jellyfish, a great gelatin consciousness everlasting".