If Beyond-5G(B5G)/6G is to support critical infrastructure worldwide, there must be an effort to jointly integrate low latency and privacy into wireless protocols. This research analyzes new schemes for securing applications at low latency by extending Physical Layer Security (PLS) algorithms to B5G/6G systems. We design protocols that advance a specific form of Physical Layer Security, known as Key-based Physical Layer Security, from the theoretical realm into the practical. One form of a Key-based algorithm obscures information from eavesdroppers by mapping it to cleverly rotated reference signals. For such a scheme, prior work has found that the two-way exchange of completely private information involves six OFDM symbol times, not including synchronization. By developing a protocol that makes the most optimum use of time-frequency resources, we show that it is possible to achieve two-way private exchange and synchronization in only four symbol times -the least latency possible. A significant simulation result indicates that our improved protocol achieves sub-1 ms two-way latency, including re-transmissions. We also illustrate a protocol that shows how Key-based Physical Layer Security can privatize critical PHY layer functions such as cell search. Lastly, additional results show the performance of the PLS algorithm in terms of Key Bit Error Rates and secret key transmission rates.