Let $G$ be a connected $n$-vertex graph in a proper minor-closed class $\mathcal G$. We prove that the extension complexity of the spanning tree polytope of $G$ is $O(n^{3/2})$. This improves on the $O(n^2)$ bounds following from the work of Wong (1980) and Martin (1991). It also extends a result of Fiorini, Huynh, Joret, and Pashkovich (2017), who obtained a $O(n^{3/2})$ bound for graphs embedded in a fixed surface. Our proof works more generally for all graph classes admitting strongly sublinear balanced separators: We prove that for every constant $β$ with $0<β<1$, if $\mathcal G$ is a graph class closed under induced subgraphs such that all $n$-vertex graphs in $\mathcal G$ have balanced separators of size $O(n^β)$, then the extension complexity of the spanning tree polytope of every connected $n$-vertex graph in $\mathcal{G}$ is $O(n^{1+β})$. We in fact give two proofs of this result, one is a direct construction of the extended formulation, the other is via communication protocols. Using the latter approach we also give a short proof of the $O(n)$ bound for planar graphs due to Williams (2002).