Copper-exchanged zeolites can continuously and selectively catalyze the partial oxidation of methane to methanol using only oxygen and water at low temperatures, but the genesis and nature of the active sites are currently unknown. Herein, we demonstrate that this reaction is catalyzed by a [Cu-O-Cu] motif that forms via a hypothesized proton-aided diffusion of hydrated Cu ions within the cages of SSZ-13 zeolites. While various Cu configurations may be present and active for methane oxidation, a dimeric Cu motif is the primary active site for selective partial methane oxidation. Mechanistically, CH activation proceeds via rate-determining C-H scission to form a surface-bound C intermediate that can either be desorbed as methanol in the presence of HO/H or completely oxidized to CO by gas-phase O. High partial oxidation selectivity can be obtained with (i) high methane and water partial pressures and (ii) maximizing Cu dimer formation by using zeolites with high Al content and low Cu loadings.