In this article, we propose the implementation of a Nonlinear Moving Horizon Estimation (NMHE) framework to estimate exogenous disturbances acting on a spacecraft for autonomous navigation around Small Celestial Bodies (SCBs). The estimation framework is coupled with a Nonlinear Model Predictive Control (NMPC) to promote robust autonomous operations in Space. The NMHE based exogenous disturbance estimation formulates a finite horizon optimization problem, while incorporating the lumped disturbances as an additional augmented state vector. Next, the estimated disturbance is utilized by the NMPC controller in a feed-forward manner. Numerous closed-loop simulations have been conducted to assess the validity of the proposed estimation and disturbance rejection framework by considering: a) Inertial hovering around two different asteroid bodies namely 433 Eros and Ryugu and b) unavailability of two primary accurate asteroid characterization data, the asteroid rotation rate na and the gravitational parameter μ. The presented results are compared with an Extended Kalman Filter (EKF) and NMPC formulation to validate the efficacy of the proposed framework.