Can I Throttle the GPU on my phone?
Most modern smartphones produce a lot of heat when playing CPU/GPU intensive games, there's not much you can do about it.

If you reduce GPU frequency, two things can happen: stuttering of gameplay (depending on your game), and the CPU/GPU run at maximum frequency for longer amounts of time to complete the same work (that a higher frequency GPU would have done in shorter time). That may negate much of the heat reduction you are trying to achieve. My 2 cents is to leave the settings at stock.

(for more details, read http://forum.xda-developers.com/showpost.php?p=34153152&amp;postcount=15576 by a chip designer who worked with Nvidia, TI etc). 

If you are still keen on underclocking, http://forum.xda-developers.com/showthread.php?t=1827635 suggests that GPU over/underclocking is possible with SetCPU app. That link is for Galaxy S3, but it should work for your phone too if your kernel supports it (you might have to flash a custom kernel to control the GPU).