Due to the supply chain globalization of the semiconductor industry, securing heterogeneous System-on-Chip (SoC) is becoming necessary. A malicious alteration, inserting Hardware Trojan, infringement, or counterfeiting of design via Reverse Engineering (RE) is the primary reason. As RE allows attackers to uncover proprietary algorithms, design specifications, and other intellectual property, exploiting the design becomes easier. This has a havoc impact on the manufacturer’s revenue as well as erodes consumer trust in the authenticity of the devices. This enforces a robust framework from the topmost design abstraction level to protect against RE attacks. This paper proposed a robust, architectural synthesis-driven dual-phase functional obfuscation framework for securing Register Transfer Level design. In this framework, obfuscation is achieved for both the datapath (DP) and control unit (CU) of design. Further, the robustness of obfuscated design is tested against sophisticated DP & CU level attacks. Moreover, to protect the design from brute force attack, a Consecutive Design Mis-Authentication Prevention Mechanism (CDMAP) is proposed. The proposed framework is validated using six standard Hardware Accelerator (HA) benchmarks and evaluated based on design overhead and robustness for different key sizes. A significant improvement is achieved in terms of security (∼ 1800 times) & (∼ 5.2 times) and strength of obfuscation (∼ 1.87×10
56
times) & (∼ 5.94×10
33
times) at a lower design cost of around (∼ 20.4%) & (∼ 10.4%) compared to two closely related approaches.