We consider the ground state of a bilayer system of dipolar bosons, where dipoles are oriented by an external field in the direction perpendicular to the parallel planes. Quantum Monte Carlo methods are used to calculate the ground-state energy, the one-body and two-body density matrix, and the superfluid response as a function of the separation between layers. We find that by decreasing the interlayer distance for fixed value of the strength of the dipolar interaction, the system undergoes a quantum phase transition from a single-particle to a pair superfluid. The single-particle superfluid is characterized by a finite value of both the atomic condensate and the super-counterfluid density. The pair superfluid phase is found to be stable against formation of many-body cluster states and features a gap in the spectrum of elementary excitations.