We investigate the properties of a single substitutional Mn impurity and its associated acceptor state on the (111) surface of Bi$_2$Se$_3$ topological insulator. Combining ab initio calculations with microscopic tight-binding modeling, we identify the effects of inversion-symmetry and time-reversal-symmetry breaking on the electronic states in the vicinity of the Dirac point. In agreement with experiments, we find evidence that the Mn ion is in the ${+2}$-valence state and introduces an acceptor in the bulk band gap. The Mn-acceptor has predominantly $p$-character, and is localized mainly around the Mn impurity and its nearest-neighbor Se atoms. Its electronic structure and spin-polarization are determined by the hybridization between the Mn $d$-levels and the $p$-levels of surrounding Se atoms, which is strongly affected by electronic correlations at the Mn site. The opening of the gap at the Dirac point depends crucially on the quasi-resonant coupling and the strong real-space overlap between the spin-chiral surface states and the mid-gap spin-polarized Mn-acceptor states.
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