The field of silicon (Si) photonic micro-electromechanical system (MEMS) for photonic integrated circuits (PICs) has evolved rapidly. Thanks to the ultra-low power consumption of Si photonic MEMS, it enables a wide range of high-performance photonic devices such as integrated optical MEMS phase shifters, tunable couplers and switches. However, photonic MEMS have suspended and movable parts which need to be protected from environmental influences, such as exposure to dust and humidity. Therefore, a packaging solution is needed for reliable operation over long periods. Here, we demonstrate wafer-level vacuum sealing of Si photonic MEMS inside cavities with ultra-thin Si caps.