Most work in privacy-preserving federated learning (FL) has been focusing on horizontally partitioned datasets where clients share the same sets of features and can train complete models independently. However, in many interesting problems, individual data points are scattered across different clients/organizations in a vertical setting. Solutions for this type of FL require the exchange of intermediate outputs and gradients between participants, posing a potential risk of privacy leakage when privacy and security concerns are not considered. In this work, we present vFedSec - a novel design with an innovative Secure Layer for training vertical FL securely and efficiently using state-of-the-art security modules in secure aggregation. We theoretically demonstrate that our method does not impact the training performance while protecting private data effectively. Empirically results also show its applicability with extensive experiments that our design can achieve the protection with negligible computation and communication overhead. Also, our method can obtain 9.1e2 ~ 3.8e4 speedup compared to widely-adopted homomorphic encryption (HE) method.