Applying in-plane uniaxial pressure to strongly correlated low-dimensional systems has been shown to tune the electronic structure dramatically. For example, the unconventional superconductor Sr$_2$RuO$_4$ can be tuned through a single Van Hove singularity which results in a strong enhancement of both $T_\text{c}$ and $H_\text{c2}$. Out-of-plane ($c$ axis) uniaxial pressure is expected to tune the quasi-two-dimensional structure even more strongly, causing it to approach two Van Hove singularities simultaneously. Here we achieve a record value of $3.2$ GPa compression along the $c$ axis of Sr$_2$RuO$_4$. Although the rise in $H_\text{c2}$ shows that we are indeed approaching the van Hove points, $T_\text{c}$ is suppressed, a result that contradicts expectations based on simple two-dimensional models. As a first attempt to take the third dimension into account, we present three-dimensional calculations in the weak interaction limit, and discuss the extent to which they are consistent with observation. Our experimental results highlight the importance of out-of-plane effects in low-dimensional systems in general and provide new constraints on theories of the pairing interaction in Sr$_2$RuO$_4$.