Accurately estimating the probability of failure for safety-critical systems is important for certification. Estimation is often challenging due to high-dimensional input spaces, dangerous test scenarios, and computationally expensive simulators; thus, efficient estimation techniques are important to study. This work reframes the problem of black-box safety validation as a Bayesian optimization problem and introduces an algorithm, Bayesian safety validation, that iteratively fits a probabilistic surrogate model to efficiently predict failures. The algorithm is designed to search for failures, compute the most-likely failure, and estimate the failure probability over an operating domain using importance sampling. We introduce a set of three acquisition functions that focus on reducing uncertainty by covering the design space, optimizing the analytically derived failure boundaries, and sampling the predicted failure regions. Mainly concerned with systems that only output a binary indication of failure, we show that our method also works well in cases where more output information is available. Results show that Bayesian safety validation achieves a better estimate of the probability of failure using orders of magnitude fewer samples and performs well across various safety validation metrics. We demonstrate the algorithm on three test problems with access to ground truth and on a real-world safety-critical subsystem common in autonomous flight: a neural network-based runway detection system. This work is open sourced and currently being used to supplement the FAA certification process of the machine learning components for an autonomous cargo aircraft.