We compute the sin(2ϕ − ϕs) azimuthal asymmetry in the pion-nucleon induced Drell-Yan process within transverse momentum dependent factorization. We employ the holographic light-front pion wave functions to calculate its leading-twist transverse momentum dependent parton distributions (TMDs). The Boer-Mulders TMD of the pion is then convoluted with the transversity TMD of the proton evaluated in a light-front quark-diquark model constructed with the wave functions predicted by the soft-wall AdS/QCD to obtain the azimuthal asymmetry in the Drell-Yan process. The gluon rescattering is pivotal to predict nonzero pion Boer-Mulders TMD. We investigate the utility of a nonperturbative SU(3) gluon rescattering kernel going beyond the usual approximation of perturbative U(1) gluons. The holographic light-front QCD approach provides a powerful tool for exploring the role of nonperturbative QCD effects in the Drell-Yan process and may help to guide future experimental measurements.