The goal of this answer is to use Moishe Kohan's idea to prove the general statement for not-necessarily-closed submanifolds. In fact even more than that can be said.
Let $M$ be a metrizable topological manifold and let $f: S \to M$ be a continuous injection from a second-countable topological manifold with $\dim S \leq \dim M - 2$. (Notice that this need not be an embedding. For instance, $f$ could be a map from $\Bbb Z^2$ with image $\Bbb Q^2 \subset M$.)
Theorem: $M \setminus f(S)$ is path-connected. In fact, for any two points $x,y \in M \setminus f(S)$, and any continuous path $\gamma: [0,1] \to M$ with $\gamma(0) = x$ and $\gamma(1) = y$, there is an arbitrarily close continuous path with the same endpoints whose image is contained in $M \setminus S$.
Remark. Injectivity is necessary because of the existence of space-filling curves. Second-countability is necessary as otherwise one could take $S$ to be $M$ equipped with the discrete topology, and $f$ to be the canonical injection.
Lemma: If $D$ is a closed disc embedded in $M$ of dimension $\dim D \leq \dim M - 2$ and $x, y \in M \setminus D$, write $\mathcal P_{x \to y} M$ for the space of continuous paths from $x$ to $y$ in $M$. Then $\mathcal P_{x \to y} (M \setminus D)$ is open and dense in $\mathcal P_{x \to y} M$.
Proof: because $S$ is closed in $M$, the set of paths with image in $M \setminus D$ is open in the compact-open topology (by definition).
Denseness is more difficult. Suppose $\gamma: [0,1] \to M$ is a continuous path with $\gamma(0) = x$ and $\gamma(1) = y$. Then $\gamma^{-1}(D)$ is a closed subset of $[0,1]$ not including the endpoints.
Fix $\epsilon > 0$. We will construct a path $\eta$ with $d_\infty(\gamma, \eta) \leq \epsilon$ and $\eta^{-1}(D) = \varnothing$. Carrying out this construction for all $\eta$ proves the desired density result.
Using the Lebesgue number lemma, one may find $n$ large so that
$\gamma([i/n, (i+1)/n]$ has diameter less than $\epsilon/2$ for all $0 \leq i < n$.
Write $U_{\epsilon,i} \subset M$ for the open set of points $$\{x \in M \mid \text{sup}_{t \in [i/n, (i+1)/n]} d(\gamma(t), x) < \epsilon\}.$$
For each $0 < i < n$ pick $x_i \in U_{\epsilon,i} \setminus D$. This exists because otherwise $D$ would contain an open subset of $M$, contradicting its dimension and the invariance of domain theorem. Set $x_0 = x$ and $x_n = y$.
Using Moishe Kohan's result, for each $0 \leq i < n$ there exists a path $\eta_i: [i/n, (i+1)/n] \to U_{\epsilon, i} \setminus D$ with $\eta_i(i/n) = x_i$ and $\eta_i\left(\frac{i+1}{n}\right) = x_{i+1}$.
Notice that $d_\infty(\eta_i, \gamma|_{[i/n, (i+1)/n]}) < \epsilon.$
Now define $\eta(t)$ to be $\eta_i(t)$ whenever $i/n \leq t \leq (i+1)/n$. Notice that this gives a well-defined continuous path on all of $[0,1]$, with $$d_\infty(\eta, \gamma) < \epsilon,$$ and with $\eta$ missing $D$, as desired.
To prove the Theorem, write $S$ as the union of countably many closed discs $D_i$. Because the domain is compact and the codomain is Hausdorff, $f$ gives a homeomorphism of $D_i$ onto $f(D_i)$. We have already seen that $\mathcal P_{x \to y} [M \setminus f(D_i)]$ is dense in $\mathcal P_{x \to y} M$. But $$\mathcal P_{x \to y} [M \setminus f(S)] = \bigcap_i \mathcal P_{x \to y} [M \setminus f(D_i)].$$
This is an intersection of countably many open dense sets inside the complete metric space $\mathcal P_{x \to y} M$. Complete metric spaces are Baire, and hence this intersection is once again dense and in particular nonempty. The theorem follows.