We investigate instanton effects on the heavy-quark potential, including its spin-dependent part, based on the instanton liquid model. Starting with the central potential derived from the instanton vacuum, we obtain the spin-dependent part of the heavy-quark potential. We discuss the results of the heavy-quark potential from the instanton vacuum. Finally, we solve the nonrelativistic two-body problem, associated with the heavy-quark potential from the instanton vacuum. The instanton effects on the quarkonia spectra are marginal but are required for quantitative description of the spectra.