Let $S:=T^2\setminus{\rm int}(D^2)$ be the torus minus an open disk. Must every continuous function $f:S\to S$ have a fixed point?
This is essentially the conclusion of the Brouwer fixed point theorem. However, that theorem only applies to spaces homeomorphic to $D^n$, and so I can't directly apply it to this question. On the other hand, I can't come up with a counterexample either.
Let's express $T^2$ by letting $H \subset \mathbb{R}^2$ be a regular hexagon centered at the origin, and then gluing opposite sides of $H$ by translations.
Let $q : H \to T^2$ be the quotient map of this gluing.
Let $D^2 \subset \mathbb{R}^2$ be a small round open disc centered at the origin and contained in the interior of $H$, and so we may regard $D^2$ as embedded in $T^2$ by the map $q$. Then, as you say, we remove the interior of $D^2$ to obtain the surface $S$.
Now let $R : H \to H$ be a rotation of angle $2 \pi / 6$. The map $R$ induces a homeomorphism $S \mapsto S$ having no fixed points.