Controlling and manipulating the polarization state of a light beam is crucial in applications ranging from optical sensing to optical communications, both in the classical and quantum regime, and ultimately whenever interference phenomena are to be exploited. In addition, many of these applications present severe requirements of phase stability and greatly benefit from a monolithic integrated-optics approach. However, integrated devices that allow arbitrary transformations of the polarization state are very difficult to produce with conventional lithographic technologies. Here we demonstrate waveguide-based optical waveplates, with arbitrarily rotated birefringence axis, fabricated by femtosecond laser pulses. To validate our approach, we exploit this component to realize a compact device for the quantum state tomography of two polarization-entangled photons. This work opens perspectives for integrated manipulation of polarization-encoded information with relevant applications ranging from integrated polarimetric sensing to quantum key distribution.