We present a combination of density functional theory and dynamical mean-field theory (DMFT) for computing the electron transmission through two-terminal nanoscale devices. The method is then applied to metallic junctions presenting alternating Cu and Co layers, which exhibit spin-dependent charge transport and the giant magnetoresistance (GMR) effect. The calculations show that the coherent transmission through the $3d$ states is greatly suppressed by electron correlations. This is mainly due to the finite lifetime induced by the electron-electron interaction and is directly related to the imaginary part of the computed many-body DMFT self-energy. At the Fermi energy, where in accordance with the Fermi-liquid behavior the imaginary part of the self-energy vanishes, the suppression of the transmission is entirely due to the shifts of the energy spectrum induced by electron correlations. Based on our results, we finally suggest that the GMR measured in Cu/Co heterostructures for electrons with energies about 1 eV above the Fermi energy is a manifestation of dynamical correlation effects.