1. A method for controlling an operation of a vapor compression system (VCS), comprising: determining, in response to receiving at least one value of a setpoint, values of measured outputs of the operation of the VCS, the measured outputs including at least one performance output controlled according to the value of the setpoint and at least one constrained output controlled to satisfy constraints independent from the value of the setpoint; determining states of the VCS using an estimator model of the VCS defining a relationship between the states of the VCS, control inputs and controlled outputs, such that a difference between outputs predicted using the estimator model and the measured outputs asymptotically approaches zero, wherein the states of the VCS include a main state representing the operation of the VCS and an auxiliary state representing the effect of unknown disturbances on each measured output of the VCS; determining an estimator relationship between the control inputs, measured disturbances, the measured outputs, and the main states of the VCS; augmenting the estimator relationship with p auxiliary states to produce the estimator model, wherein p is a number of the measured outputs, and wherein the auxiliary states represent an aggregate effect of the unknown disturbances and uncertainties on the measured outputs at a steady operating condition of the VCS; and determining control inputs for controlling the operation of the VCS using a prediction model defining a relationship between the states of the VCS, the control inputs, the performance and constrained outputs, and the value of the setpoint, such that the constrained output satisfies the constraints, and a difference between the performance output and the value of the setpoint asymptotically approaches zero; and controlling the operation of the VCS according to the control inputs, wherein steps of the method are performed by a processor.