The integration of wireless power transfer (WPT) with massive multiple-input multiple-output (MIMO) non-orthogonal multiple access (NOMA) networks can provide operational capabilities to energy-constrained Internet of Things (IoT) devices in cyber-physical systems such as smart autonomous vehicles. However, during downlink WPT, co-channel interference (CCI) can limit the energy efficiency (EE) gains in such systems. This paper proposes a user equipment (UE)–base station (BS) connection model to assign each UE to a single BS for WPT to mitigate CCI. An energy-efficient resource allocation scheme is developed that integrates the UE–BS connection approach with joint optimization of power control, time allocation, antenna selection, and subcarrier assignment. The proposed scheme improves EE by 24.72% and 33.76% under perfect and imperfect CSI conditions, respectively, compared to a benchmark scheme without UE–BS connections. The scheme requires fewer BS antennas to maximize EE and the distributed algorithm exhibits fast convergence. Furthermore, UE–BS connections’ impact on EE provided significant gains. Dedicated links improve EE by 24.72% (perfect CSI) and 33.76% (imperfect CSI) over standard connections. Imperfect CSI reduces EE, with the proposed scheme outperforming by 6.97% to 12.75% across error rates. More antennas enhance EE, with improvements of up to 123.12% (conventional MIMO) and 38.14% (massive MIMO) over standard setups. Larger convergence parameters improve convergence, achieving EE gains of 7.09% to 11.31% over the baseline with different convergence rates. The findings validate the effectiveness of the proposed techniques in improving WPT efficiency and EE in wireless-powered MIMO–NOMA networks.