As autonomous systems become more complex and integral in our society, the need to accurately model and safely control these systems has increased significantly. In the past decade, there has been tremendous success in using deep learning techniques to model and control systems that are difficult to model using first principles. However, providing safety assurances for such systems remains difficult, partially due to the uncertainty in the learned model. In this work, we aim to provide safety assurances for systems whose dynamics are not readily derived from first principles and, hence, are more advantageous to be learned using deep learning techniques. Given the system of interest and safety constraints, we learn an ensemble model of the system dynamics from data. Leveraging ensemble uncertainty as a measure of uncertainty in the learned dynamics model, we compute a maximal robust control invariant set, starting from which the system is guaranteed to satisfy the safety constraints under the condition that realized model uncertainties are contained in the predefined set of admissible model uncertainty. We demonstrate the effectiveness of our method using a simulated case study with an inverted pendulum and a hardware experiment with a TurtleBot. The experiments show that our method robustifies the control actions of the system against model uncertainty and generates safe behaviors without being overly restrictive. The codes and accompanying videos can be found on the project website.