We calculate the spin-dependent potential, which is the $𝒪(1/M^2)$ correction term to the thermal potential between a static quark-antiquark pair within non-relativistic QCD. At leading order in hard thermal loop perturbation theory, we show that this spin-dependent potential has an imaginary part which is different in magnitude for pseudoscalar and vector quarkonium states. For the first time, we extract the imaginary part non-perturbatively using lattice techniques, in the deconfined phase of quenched QCD at $T\sim 470$ MeV, after performing a continuum estimation and subsequent renormalization. We have found that the spin-dependent potential in the quark-gluon plasma phase is complex, and its imaginary part has a remarkably significant contribution over the thermal static potential for charmonium states. Consequences of this thermal spin-dependent potential on the quarkonium spectral functions are also discussed.