I think magic would win since it takes less energy to create an effect which might have required vast resources and knowledge for super science to duplicate. For example, to travel through time via superscience would require building a time machine or some form of time manipulation device. With magic, the will would lead to the result, so a magical being could shrug and go backwards or forwards in time. As Kid Weather pointed out, magic is connected to the imagination and your ability to intuitively understand what you are doing, whereas super science is connected to knowledge, resources and knowledge.
Just wanted to say that tron_Bonne said it. Anyways what would happen if a time machine or what ever was already at the super scientist behest