We theoretically study the effect of low-frequency light pulses in resonance with phonons in the topological and magnetically ordered two septuple-layer (2-SL) MnBi2Te4 (MBT) and MnSb2Te4 (MST). These materials share symmetry properties and an antiferromagnetic ground state in pristine form but present different magnetic exchange interactions. In both materials, shear and breathing Raman phonons can be excited via non-linear interactions with photo-excited infrared phonons using intense laser pulses attainable in current experimental setups. The light-induced transient lattice distortions lead to a change in the sign of the effective interlayer exchange interaction and magnetic order accompanied by a topological band transition. Furthermore, we show that moderate anti-site disorder, typically present in MBT and MST samples, can facilitate such an effect. Therefore, our work establishes 2-SL MBT and MST as candidate platforms to achieve non-equilibrium magneto-topological phase transitions.