It is a challenging task to deploy lightweight security protocols in resource-constrained IoT applications. A hardware-oriented lightweight authentication protocol based on device signature generated during voltage over-scaling (VOS) was recently proposed to address this issue. VOS-based authentication employs the computation unit such as adders to generate the process variation dependent error which is combined with secret keys to create a two-factor authentication protocol. In this paper, machine learning (ML)-based modeling attacks to break such authentication is presented. We also propose a dynamic obfuscation mechanism based on keys (DOMK) for the VOS-based authentication to resist ML attacks. Experimental results show that ANN, RNN and CMA-ES can clone the challenge-response behavior of VOS-based authentication with up to 99.65% predication accuracy, while the predication accuracy is less than 51.2% after deploying our proposed ML resilient technique.