Agree with Douglas, if part of your body's telling you to call time on your session then listen to it. People talk about 'endurance' in guitar playing but you don't build it up by deliberately practising until your hands hurt and then keeping going - playing the guitar isn't the same as distance running or fitness-dependant sports.

That said, a friend of mine swears by cold showers for reducing tissue damage after running distances, and although I personally can't stand this and have never known it work for me, I found that putting my left hand and wrist in a bowl of iced water after a guitar practice session where I realised I'd overdone it helped. I've used that ever since.

Here's another idea for you while we're on the subject: guitarists almost always talk about warming up by playing scales or exercises, which I myself do, but what I almost never hear talked about is warming up muscles before you've even picked up the guitar. A couple of years ago I saw an excerpt from John Petrucci's Rock Discipline video where he actually advocated doing certain stretches before picking the instrument up, to date he's the only guitarist I've ever seen promote this.

I decided to take this idea a stage further, remembering how a sports coach once advised me never to stretch muscles when they're cold, always warm up with something like a run on aerobic exercise before you stretch, so I warmed up like this, went for a steady run after it and then stretched some more to cool down before I went in and picked up the guitar to see what it felt like. The result was amazing! I admit that I'm pretty hard-wearing on my whole body as I'm the outdoors type, constantly active and both my job and other hobbies have me lifting stuff and making stuff, and I often wake up with various bits of me aching, so I have to loosen up to do anything comfortably let alone play a guitar.

If anything I find that before my fretboard hand gets too tired to keep going my left shoulder's giving me trouble just from the weight of the guitar (and I play an Ibanez JS most of the time, which comparatively is the featherweight end of guitars) I can usually last an hour and a half or so without unstrapping the guitar - I prefer to play standing, sitting down I get uncomfortable more quickly and the whole technique feels more controlled standing....not entirely sure why.

On a different note, I came to realise that making changes to the way I play to avoid discomfort actually added something to my playing style in some ways - I don't do a lot of string bending and I think it's partly because I found it made my fingers sore quickly, so to extend how long I could practice for I took to using sliding and hammer-ons more to quick pitch shifting, and my use of the Floyd Rose became different as I used it to save my fingers....my hands ache just listening to some players like Walter Trout who bend strings as if they could never snap in just about every song.