I am surprised, because I can bake multiple materials in cycles in blender 2.76b. The important thing I have to select an active image for all the materials linked to the object, and they can be different images. Active image is the selected one in the node setup of the material. So select a different image for the procedural textured. Please try it.
The selected image is the active, and not necessarily connected to the node graph. However you must select one for all of the materials of your object
If it fails try this instead
Make a duplicate from your character, delete all the materials except the one with the procedural texture. You will get the texture with baking, however it will be all over your UV map, but you can make a mask for it with a next bake
Use a pure white material instead of the procedural textured, and a pure dark for the others. You can use this mask to recover the wanted result from the previous bake.