In this study, we used the heat-sensitive stony coral Pocillopora acuta and show that three-day exposure to sublethal temperature increases thermal tolerance during subsequent acute thermal stress via modulations in programmed cell death pathways. In preconditioned corals, the expression of pro-survival gene pa-Bcl-2 increases relative to pro-death genes pa-Bak and pa-Bax during the early phase of the thermal stress. After pa-Bcl-2 activity inhibition, preconditioned corals lose the acquired phenotype and bleach at the same rate as non-preconditioned corals, which determines the pivotal role of pa-Bcl-2 and programmed cell death in coral bleaching and acclimatization. The detailed analysis points to the involvement of autophagy/symbiophagy rather than apoptosis in the process. Corals exposed to natural oceanic summer temperatures show stress-induced gene expression profile similar to the experimentally preconditioned corals which suggests that during periods with a high probability of extreme temperature events, corals can naturally increase their resilience through alterations in cell signaling.