Impurities added by the sages

Hello Rabbi Michael, 
It is known that there are defilements that the Sages decreed on their own, not out of any fear of impurity, as they decreed for impurity of hands (which are businesslike) or impurity of the land of the nations (which are not at all careful about impurity and purity). Rather, they are defilements that the Sages "invented" in order to restrict certain behavior and therefore decreed it. 
An example of this is a Torah scroll that defiles the hands and in effect negates the impurity, since in their day they placed the offering together with the Torah scroll and mice (or other animals) would come and gnaw on the Torah scroll as well. In this way, the Sages established impurity on Gentiles who would be false so that Israel would not associate with them, despite the Torah saying that a Gentile simply does not defile.
 
My question is, where does the Sages have the authority to deduce such impurity? Simply put, even if we don't understand all the reasons for the laws of impurity and purity, we can see that there is a metaphysical-spiritual reality here that the Torah established and wrote... So where did the Sages come from and "invent" new impurities that the Torah did not speak of? And one must also ask how there is no "you shall not add" to what the Torah has already established? After all, it is not to distance oneself from impurity, but for other purposes altogether.