According to the book I'm reading (Introduction to $3$-manifolds, by Jennifer Schultens),
A submanifold $A$ of a connected manifold $X$ is separating if $X \setminus A$ has at least two components; otherwise it is non-separating.
The remark following this definition reads:
Connected manifolds are path connected. It follows that a submanifold $A$ of a connected manifold $X$ is non-separating if and only if there is a simple closed curve in $X$ that intersects $A$ transversely in a single point.
I was able to prove that if $A$ is non-separating then such a curve exists. Could you give me any hints on how to prove the converse?
Intersection numbers of submanifolds are well-defined in homology (that is, if you're taking the intersection number of $S$ and $L$, replacing $S$ with the homologous $S'$ gives the same intersection number). A separating submanifold is null-homologous, so the intersection number with any curve is automatically zero.
In more elementary language: Let $M$ be one side of the separating submanifold $S$. Suppose $L$ is a submanifold of the opposite codimension that intersects $S$ transversely. Then $L \cap M$ is also a transverse intersection of oriented manifolds, so is an oriented compact 1-manifold with oriented boundary $L \cap S$; but because the oriented number of points on the boundary of any compact 1-manifold is $0$, the intersection number coming from $L \cap S$ is zero.