Recent technological advancements in computing, sensing and communication have led to the development of cyber-physical manufacturing processes, where a computing subsystem monitors the manufacturing process performance in real-time by analyzing sensor data and implements the necessary control to improve the product quality. This paper develops a predictive control framework where control actions are implemented after predicting the state of the manufacturing process or product quality at a future time using process models. In a cyber-physical manufacturing process, the product quality predictions may be affected by uncertainty sources from the computing subsystem (resource and communication uncertainty), manufacturing process (input uncertainty, process variability and modeling errors), and sensors (measurement uncertainty). In addition, due to the continuous interactions between the computing subsystem and the manufacturing process, these uncertainty sources may aggregate and compound over time. In some cases, some process parameters needed for model predictions may not be precisely known and may need to be derived from real time sensor data. This paper develops a dynamic Bayesian network approach, which enables the aggregation of multiple uncertainty sources, parameter estimation and robust prediction for online control. As the number of process parameters increase, their estimation using sensor data in real-time can be computationally expensive. To facilitate real-time analysis, variance-based global sensitivity analysis is used for dimension reduction. The proposed methodology of online monitoring and control under uncertainty, and dimension reduction, are illustrated for a cyber-physical turning process.