Estimation of quantum relative entropy and its Rényi generalizations is a fundamental statistical task in quantum information theory, physics, and beyond. While several estimators of these divergences have been proposed in the literature along with their computational complexities explored, a limit distribution theory which characterizes the asymptotic fluctuations of the estimation error is still premature. As our main contribution, we characterize these asymptotic distributions in terms of Fréchet derivatives of elementary operator-valued functions. We achieve this by leveraging an operator version of Taylor's theorem and identifying the regularity conditions needed. As an application of our results, we consider an estimator of quantum relative entropy based on Pauli tomography of quantum states and show that the resulting asymptotic distribution is a centered normal, with its variance characterized in terms of the Pauli operators and states. We utilize the knowledge of the aforementioned limit distribution to obtain asymptotic performance guarantees for a multi-hypothesis testing problem.