This paper presents an approximated aggregated analytical method analysis of Stochastic Hybrid Petri Nets (SHPN) models with finite capacity buffers for evaluating the throughput of pipe-line computer systems (PCS). The method is based on decomposition of SHPN into single buffer subnets used as the building block for performance evaluation of PCS. We develop an iterative method to accurately estimate performance characteristics of PCS such as throughput and mean buffer contents. The accuracy of the proposed method has been validated by numerical simulations and experiments.