This is unfortunately a problem for players of all levels, not just beginners. The good news is once you have been playing for a while your body does adapt to what was once uncomfortable, much better. However, the unfortunate reality is that you will confront this beast throughout your entire career. I know I have.
I ran into big problems while I was in school about 5 years ago. I went from playing 1-2 hours a day to playing 8-10!!! Quite a change, and my body couldn't handle it. I saw a hand specialist, and they gave me some stretches that cured me. That mixed with not playing as much really, really helped.
Fast forward about 4 years later, and same problem. We all spend a lot of time on computers, and that only adds to the mess we can create for our arms and back. I overcame it, but again I simply had to step away from the instrument and the computer for a few weeks.
For you, I would suggest the same thing. If you are experiencing some real discomfort that is expected in the beginning. However, you need to take it easy and don't push it. If you experience this pain the minute you pick your guitar up, than I would see a hand specialist and get yourself checked out. Everything is very connected in your body, and problems in the hands and elbows can result from back issues, etc.
Do you have access to a good guitar teacher in your area that is experienced and can look at your technique if the problem persists? :confused:
Douglas Showalter