You are right, the definition doesn't apply to the empty set. What your professor should have said is that for the empty set it's defined separately as $\infty$.
Why is this a sensitive definition?
You have some properties that you would like to remain true in the case of the empty set.
For example, if $A \subseteq B$ then $\min A \ge \min B$. That's easy to prove for non-empty sets, so you would like to define it for the empty set so this remains true.
But $\emptyset \subseteq B$ for all subsets $B$, so you'll need $\min \emptyset \ge \min B$ for all subsets $B$. In particular if $B=\{x\}$, $\min \emptyset \ge x$ for all $x \in \mathbb R$. Obviously there's no such real number and this clearly motivates the defintion $\min \emptyset = \infty$.
Other properties involving union, intersection or complement of sets also can be used to motivate this definition and in general all works very nice with this definition.
Note: For subsets of $\mathbb R$ in general one should talk about the infimum, not the minimum, since not all sets have a least element.