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 n a 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.