We calculate the electromagnetic pion form factor in lattice QCD with 2+1 flavors of the dynamical overlap quarks. Up and down quark masses are set below their physical values so that the system is in the so-called ε regime with the small size of our lattice ∼1.8  fm. The finite volume corrections are generally expected to be ∼100% in the ε regime. We, however, find a way to automatically cancel the dominant part of them. Inserting nonzero momenta and taking appropriate ratios of the two- and three-point functions, we can eliminate the contribution from the zero-momentum pion mode. Then the remaining finite volume effect is a small perturbation from the nonzero modes. Our lattice data agree with this theoretical prediction and the extracted pion charge radius is consistent with the experiment.