Providing safety guarantees for learning-based controllers is important for real-world applications. One approach to realizing safety for arbitrary control policies is safety filtering. If necessary, the filter modifies control inputs to ensure that the trajectories of a closed-loop system stay within a given state constraint set for all future time, referred to as the set being positive invariant or the system being safe. Under the assumption of fully known dynamics, safety can be certified using control barrier functions (CBFs). However, the dynamics model is often either unknown or only partially known in practice. Learning-based methods have been proposed to approximate the CBF condition for unknown or uncertain systems from data; however, these techniques do not account for input constraints and, as a result, may not yield a valid CBF condition to render the safe set invariant. In this work, we study conditions that guarantee control invariance of the system under input constraints and propose an optimization problem to reduce the conservativeness of CBF-based safety filters. Building on these theoretical insights, we further develop a probabilistic learning approach that allows us to build a safety filter that guarantees safety for uncertain, input-constrained systems with high probability. We demonstrate the efficacy of our proposed approach in simulation and real-world experiments on a quadrotor and show that we can achieve safe closed-loop behavior for a learned system while satisfying state and input constraints.