Real world quantum systems are open to perpetual influence from the wider environment. Quantum gravitational fluctuations provide a most fundamental source of the environmental influence through their universal interactions with all forms of energy and matter causing decoherence. This may have subtle implications on precision laboratory experiments and astronomical observations and could limit the ultimate capacities for quantum technologies prone to decoherence. To establish the essential physical mechanism of decoherence under weak spacetime fluctuations, we carry out a sequence of analytical steps utilizing the Dirac constraint quantization and gauge invariant influence functional techniques resulting in a general master equation of a compact form that describes an open quantum gravitational system with arbitrary bosonic fields. An initial application of the theory is illustrated by the implied quantum gravitational dissipation of light as well as (non)relativistic massive or massless scalar particles. Related effects could eventually lead to important physical consequences including those on a cosmological scale and for a large number of correlated particles.