We demonstrate a 3D conductive coupling mechanism for the efficient generation of prominent and robust Fano resonances in 3D metamaterials (MMs) formed by integrating vertical U-shape split-ring resonators (SRRs) or vertical rectangular plates along a planar metallic hole array with extraordinary optical transmission (EOT). In such a configuration, intensified vertical E-field is induced along the metallic holes and naturally excites the electric resonances of the vertical structures, which form non-radiative "dark" modes. These 3D conductive "dark" modes strongly interfere with the "bright" resonance mode of the EOT structure, generating significant Fano resonances with both prominent destructive and constructive interferences. The demonstrated 3D conductive coupling mechanism is highly universal in that both 3D MMs with vertical SRRs and vertical plates exhibit the same prominent Fano resonances despite their dramatic structural difference, which is conceptually different from conventional capacitive and inductive coupling mechanisms that degraded drastically upon small structural deviations.