High-performance computing (HPC) systems are essential for scientific discovery and engineering innovation. However, their growing power demands pose significant challenges, particularly as systems scale to the exascale level. Prior uncore frequency tuning studies have primarily focused on conventional HPC workloads running on homogeneous systems. As HPC advances toward heterogeneous computing, integrating diverse GPU workloads on heterogeneous CPU-GPU systems, it is crucial to revisit and enhance uncore scaling. Our investigation reveals that uncore frequency scales down only when CPU power approaches its TDP (Thermal Design Power), an uncommon scenario in GPU-dominant applications, resulting in unnecessary power waste in modern heterogeneous computing systems. To address this, we present MAGUS, a user-transparent uncore frequency scaling runtime for heterogeneous computing. Effective uncore tuning is inherently complex, requiring dynamic detection of application execution phases that affect uncore utilization. Moreover, any robust strategy must work across a diverse range of applications, each with unique behaviors and resource requirements. Finally, an efficient runtime should introduce minimal overhead. We incorporate several key techniques in the design of MAGUS, including monitoring and predicting memory throughput, managing frequent phase transitions, and leveraging vendor-supplied power management support. We evaluate MAGUS using a diverse set of GPU benchmarks and applications across multiple heterogeneous systems with different CPU and GPU architectures. The experimental results show that MAGUS achieves up to 27% energy savings and 26% energy-delay product (EDP) reduction compared to the default settings while maintaining a performance loss below 5% and an overhead under 1%.