It has been known that the time-dependent Hartree-Fock (TDHF) method, or the time-dependent density functional theory (TDDFT), fails to describe many-body quantum tunneling. We overcome this problem by superposing a few time-dependent Slater determinants with the time-dependent generator coordinate method (TDGCM). We apply this method to scattering of two $alpha$ particles in one dimension, and demonstrate that the TDGCM method yields a finite tunneling probability even at energies below the Coulomb barrier, at which the tunneling probability is exactly zero in the TDHF. This is the first case in which a many-particle tunneling is simulated with a microscopic real-time approach.