Nowadays, photovoltaic (PV) systems based on centralized topology with a three-level T-type (3LT2) inverter are used to decrease investment costs and increase conversion efficiency. In this topology, the split capacitors of the DC-link can individually connected to PV arrays. Accordingly, DC-link capacitors’ voltage should separately controlled to track PV arrays’ maximum power point (MPP) voltage. However, the asymmetric control of capacitors’ voltage causes line voltage to unbalance and output current to distort. In this paper, a hybrid method based on dipolar variable injection and zero-sequence voltage injection concepts is proposed to simultaneously control the DC-link capacitors’ voltage of the 3LT2 inverter and eliminate their voltages ripple. In the presence of partial shading, the proposed method can control the capacitors’ voltage of the DC-link to realize the separate MPP tracking while ensuring the balance of line voltages. Furthermore, the proposed method eliminates the voltage ripple on DC-link capacitors, inherently caused by the 3LT2 inverter, to improve the DC-link lifetime and the PV system reliability. The simulation studies and practical experiments have been performed, and their results prove the validity of the proposed method, whether the PF is unity or non-unity.