Here we demonstrate how the Fermi surface topology and quantum many-body interactions can be manipulated via epitaxial strain in the spin-triplet superconductor Sr$_2$RuO$_4$ and its isoelectronic counterpart Ba$_2$RuO$_4$ using oxide molecular beam epitaxy (MBE), emph{in situ} angle-resolved photoemission spectroscopy (ARPES), and transport measurements. Near the topological transition of the $gamma$ Fermi surface sheet, we observe clear signatures of critical fluctuations, while the quasiparticle mass enhancement is found to increase rapidly and monotonically with increasing Ru-O bond distance. Our work demonstrates the possibilities for using epitaxial strain as a disorder-free means of manipulating emergent properties, many-body interactions, and potentially the superconductivity in correlated materials.