The effectiveness of measurement-based feedback control protocols is hampered by the presence of measurement noise, which affects the ability to accurately infer the underlying dynamics of a quantum system from noisy continuous measurement records to determine an accurate control strategy. To circumvent such limitations, this Letter explores a real-time stochastic state estimation approach that enables noise-free monitoring of the conditional dynamics including the full density matrix of the quantum system using noisy measurement records within a single quantum trajectory-a method we name as "conditional state tomography." This, in turn, enables the development of precise measurement-based feedback control strategies that lead to effective control of quantum systems by essentially mitigating the constraints imposed by measurement noise and has potential applications in various feedback quantum control scenarios. This approach is particularly useful for reinforcement-learning-(RL) based control, where the RL-agent can be trained with arbitrary conditional averages of observables, and/or the full density matrix as input (observation), to quickly and accurately learn control strategies.