We present a practical method for active phase control on a photonic chip that has immediate applications in quantum photonics. Our approach uses strain-optic modification of the refractive index of individual waveguides, effected by a millimeter-scale mechanical actuator. The resulting phase change of propagating optical fields is rapid and polarization-dependent, enabling quantum applications that require active control and polarization encoding. We demonstrate strain-optic control of non-classical states of light in silica, showing the generation of 2-photon polarisation N00N states by manipulating Hong-Ou-Mandel interference. We also demonstrate switching times of a few microseconds, which are sufficient for silica-based feed-forward control of photonic quantum states.