With the emergence of 5G low-latency applications, such as haptics and V2X, low-complexity and low-latency security mechanisms are needed. Promising lightweight mechanisms include physical unclonable functions (PUF) and secret key generation (SKG) at the physical layer, as considered in this paper. In this framework, we propose (i) a zero round trip time (0-RTT) resumption authentication protocol combining PUF and SKG processes, (ii) a novel authenticated encryption (AE) using SKG, and (iii) pipelining of the AE SKG and the encrypted data transfer in order to reduce latency. Implementing the pipelining at PHY, we investigate a parallel SKG approach for multi-carrier systems, where a subset of the subcarriers are used for SKG and the rest for data transmission. The optimal solution to this PHY resource allocation problem is identified under security, power, and delay constraints, by formulating the subcarrier scheduling as a subset-sum 0 − 1 knapsack optimization. A heuristic algorithm of linear complexity is proposed and shown to incur negligible loss with respect to the optimal dynamic programming solution. All of the proposed mechanisms have the potential to pave the way for a new breed of latency aware security protocols.