The perovskite unit cell is the fundamental building block of many functional materials. The manipulation of this crystal structure is known to be of central importance to controlling many technologically promising phenomena related to superconductivity, multiferroicity, mangetoresistivity, and photovoltaics. The broad range of properties that this structure can exhibit is in part due to the centrally coordinated octahedra bond flexibility, which allows for a multitude of distortions from the ideal highly symmetric structure. However, continuous and fine manipulation of these distortions has never been possible. Here, we show that controlled insertion of He atoms into an epitaxial perovskite film can be used to finely tune the lattice symmetry by modifying the local distortions, i.e., octahedral bonding angle and length. Orthorhombic SrRuO3 films coherently grown on SrTiO3 substrates are used as a model system. Implanted He atoms are confirmed to induce out-of-plane strain, which provides the ability to controllably shift the bulk-like orthorhombically distorted phase to a tetragonal structure by shifting the oxygen octahedra rotation pattern. These results demonstrate that He implantation offers an entirely new pathway to strain engineering of perovskite-based complex oxide thin films, useful for creating new functionalities or properties in perovskite materials.