In this note we present a formula for the equivariant index of the cohomological complex obtained from localization of $\mathcal{N}=2$ SYM on simply-connected compact four-manifolds with a $T^2$-action. Knowledge of said index is essential to compute the perturbative part of the partition function for the theory. In the topologically twisted case, the complex is elliptic and its index can be computed in a standard way using the Atiyah-Bott localization formula. Recently, a framework for more general types of twisting, so-called cohomological twisting, was introduced for which the complex turns out to be only transversally elliptic. While the index of such a complex has been computed for some cases where the manifold can be lifted to a Sasakian $S^1$-fibration in five dimensions, a general four-dimensional treatment was still lacking. We provide a formal, purely four-dimensional treatment of the cohomological complex, showing that the Laplacian part can be globally split off while the remaining part can be trivialized uniquely in the group-direction. This ultimately produces a simple formula for the index applicable for any compact simply-connected four-manifold. Finally, the index formula is applied to examples on $S^4$, $\mathbb{CP}^2$ and $\mathbb{F}^1$. For the latter, we use the result to compute the perturbative partition function.
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