This paper presents a novel security mechanism for sensitive data stored, acquired or processed by a complex electronic circuit implemented as System-on-Chip (SoC) on an FPGA reconfigurable device. Such circuits are increasingly used in embedded or cyber systems employed in civil and military applications. Managing security in the overarching SoC presents a challenge as part of the process of securing such systems. The proposed new method is based on encrypted and authenticated communications between the microprocessor cores, FPGA fabric and peripherals inside the SoC. The encryption resides in a key generated with Physically Unclonable Function (PUF) circuits and a pseudorandom generator. The conceptual design of the security circuit was validated through hardware implementation, testing and analysis of results.