The emergence of time and wavelength division multiplexed-passive optical network (TWDM-PON) architectures as next-generation access network technologies necessitates the development of new types of network devices and enhanced agile mechanisms. In this paper, we propose a software-defined (SD) TWDM-PON architecture in which legacy PON devices are enriched with SD capabilities. In the proposed architecture, SD orchestration is used to coordinate the wavelength/link-rate deployments and to enable energy-efficient operations by switching the OLT/ONU transceivers to a lower link rate or turning them off in low traffic conditions while maintaining the necessary QoS. We provide system performance and energy-savings trade-off analysis and compare the delay, throughput, and drop probability with the energy-savings performance in the OLT and ONU for various scenarios.