The file which is responsible for this feature is ".Xmodmap" in the home folder (just open the home folder and hit Ctrl + H and you will see it). If you open this file with gedit, you will see it is like this:
pointer = 1 2 3 5 4 6 7 8 9 10 11 12
As you notice, 5 is placed before 4 in the sequence and this makes the "natural scrolling" happen. If you switch the sequence back to the normal order (4 before 5) or just delete this ".Xmodmap" file then log out and log in, the natural scrolling feature will be disabled.
Note: but if you are using another distro and want to enable this feature in your distro, just open the text editor and create the file ".Xmodmap" with the switched sequence like above and save it in the home folder, then log out and log in and "natural scrolling" will be enabled in your distro.