Yes, but the button layout's a bit off. You have to hit F2 on the main menu and adjust it there. Also, the left analog stick is the one that's used for moving, which makes it tougher to pull of specials and fatalities. I haven't found a way to change it to the D-pad yet in-game, so keep that in mind.

Of course, you can always use a program like Joy2Key and map things out on the controller that way after setting the game to use the keyboard for its controls. Then you could use the D-pad for movement once you've mapped everything in Joy2Key (or whatever program you'd use).

I found a better way IMHO :)
https://www.gog.com/forum/mortal_kombat/using_dpad_for_control_instead_of_analog_in_mk4