We present calculations of the one-loop vacuum polarization correction (Uehling potential) for the three-body problem in the NRQED formalism. The case of one-electron molecular systems is considered. Numerical results of the vacuum polarization contribution at mα7 and higher orders for the fundamental transitions (v = 0, L = 0) → (v ′ = 1, L ′ = 0) in the H2+ and HD+ molecular ions are presented and compared with calculations performed in the adiabatic approximation. The residual uncertainty from this contribution on the transition frequencies is shown to be of a few tens of Hz.