Confinement and chiral symmetry breaking remain two the most interesting and challenging nonperturbative phenomena in non-Abelian gauge theories. Recent semiclassical (for $SU(2)$) and lattice (for QCD) studies have suggested that confinement arises from interactions of statistical ensembles of instanton dyons with the Polyakov loop. In this proceeding, recent work is presented which has extended the study of semiclassical ensemble of dyons to the $SU(3)$ Yang-Mills theories with $N_f=0$ and $N_f=2$ flavors of massless, dynamical quarks. Dynamical quarks are included via the interaction of their topological zero modes on the dyons. It will be shown that such interactions do generate the expected first-order deconfinement phase transition in the $N_f=0$ case and are compatible with a second-order transition in the $N_f=2$ case. Studying the Dirac eigenvalue spectrum at multiple system sizes reveals that the overlap of the quark zero modes generates a nonzero condensate below $T_c$, breaking chiral symmetry.