The spectrum of Internet of Things (IoT) applications is vast. It serves in various domains such as smart homes, intelligent buildings, health care, emergency response, and many more, reflecting the exponential market penetration of the IoT. Various security threats have been made to modern-day systems. Cyberattacks have seen a marked surge in frequency, particularly in recent times. The growing concern centers around the notable rise in cloning attacks, persisting as a significant and looming threat. In our work, an in-depth survey on the IoT that employs physically unclonable functions (PUFs) was conducted. The first contribution analyzes PUF-based authentication, communication protocols, and applications. It also tackles the eleven challenges faced by the research community, proposes solutions to these challenges, and highlights cloning attacks. The second contribution suggests the implementation of a framework model known as PUF3S-ML, specifically crafted for PUF authentication in the Internet of Things (IoT), incorporating innovative lightweight encryption techniques. It focuses on safeguarding smart IoT networks from cloning attacks. The key innovation framework comprises three stages of PUF authentication with IoT devices and an intelligent cybersecurity monitoring unit for IoT networks. In the methodology of this study, a survey relevant to the concerns was conducted. More data were provided previously regarding architecture, enabling technologies, and IoT challenges. After conducting an extensive survey of 125 papers, our analysis revealed 23 papers directly relevant to our domain. Furthermore, within this subset, we identified 11 studies specifically addressing the intersection of communication protocols with PUFs. These findings highlight the targeted relevance and potential contributions of the existing literature to our research focus.