Open a terminal and issue this command as root:
# modprobe -r pcspkr snd_pcsp
To prevent the "pcspkr" and "snd_pcsp" modules from loading again at startup add them to modprobe's blacklist in /etc/modprobe.d/blacklist. You can do this with the following command:
# vi
blacklist pcspkr
blacklist snd_pcsp
See: http://www.thinkwiki.org/wiki/How_to_disable_the_pc_speaker_(beep!)