This paper concerns the design of an energy management system for a building cooling system that includes a chiller plant (with two or more chiller units), a thermal storage unit, and a cooling load. The latter is modeled in a probabilistic framework to account for the uncertainty in the building occupancy. The energy management task essentially consists in the minimization of the energy consumption of the cooling system, while preserving comfort in the building. This is achieved by a twofold strategy. The cooling power request is optimally distributed among the chillers and the thermal storage unit. At the same time, a slight modulation of the temperature set-point of the zone is allowed, trading energy saving for comfort. The problem can be decoupled into a static optimization problem (mainly addressing the chiller plant optimization) and a dynamic programming (DP) problem for a discrete time stochastic hybrid system (SHS) that takes care of the overall energy minimization. The DP problem is solved by abstracting the SHS to a (finite) controlled Markov chain, where costs associated with state transitions are computed by simulating the original model and determining the corresponding energy consumption. A numerical example shows the efficacy of the approach.