What you'll need to do is add a Fitness coach to the side and improve it as much as you can. This could take some time however, so for now you'll just have to make sure you sub your weakest players at the right moments in games, until you manage to get your fitness coach' effectiveness up. Once the Fitness Coach is at a good standard your players should be able to play through every game without getting too tired.
Another thing to keep in mind is when the next transfer window opens, you may want to focus on buying players with higher fitness levels.