Try to plan ahead when you'll stop with a timer or something, and make sure it's before you get tired because:
a. if your hands get too tired it could lead to injury.
b, if your brain gets too tired or simply bored you'll lose concentration, which will lead to mistakes. You can tell by your ear that you're making mistakes but your muscles cannot, so through repetitions you'll incorporate those mistakes, along with the frustration and tension that they cause, into your playing.
The most part of learning and getting familiar with a piece happens away from the piano, so practice for not too long (2 to 20 minutes) on one or two phrases in particular (remember to alternate hands to avoid tiring) and leave that for the day, next session jump to something else and don't practice a part again until the next day, and you'll notice how it is far easier than it was the day before. Repeat the same proceedure and you'll get to the point where you don't need practice to get the physical aspect to feel natural.
Sometimes practicing is like painting a wall: you must give it a few layers of paint to get it looking right, but you can spend a whole day painting the same spot and it'll be a waste of time; it's best to cover it with one layer, let it dry and apply the next layer the following day.