Here's my shot at defining time: if you think into the core meaning of time, time is really only change. When something changes, time is "passing." Since everything in our universe is always in a state of flux, time is always passing. Time can "pass" faster or slower because matter/energy is changing, or doing something, faster or slower. The rate of change is due, as arunma has pointed out, to the bending of space.

Now consider the Golden Goddesses. To be considered a god/goddess, one must be perfect, correct? Some aspects of perfection are omnipotence (all-powerful) and enternality (infinite and unchanging). Since the goddesses are omnipotent, it wouldn't be a stretch to say that they can work with infinite energy. Since it takes infinite energy to travel back in time, like arunma says, the goddesses can make time go in reverse.

But what if nothing changes? Theoretically, there would be no time. Time would not be a valid consideration. Now, since a perfect being is infinite, eternal, and unchanging, that must mean that this perfect being TRANSCENDS time. The Golden Goddesses (or the Goddess of Time, perhaps) CREATED time, and thus can manipulate it however they want to. This also means that objects imbued with the power of the goddesses can be used to manipulate time.  The Ocarina of Time, the Master Sword, etc., all must use the power of the goddesses to control time.

What do you guys think of these theories?