High temperature is a significant abiotic stress that affects growth and development of plants. BAG (Bcl-2 associated athanogene) protein family members act as co-chaperones and apoptosis inhibitors in multiple cellular processes. BAG, MAPK (Mitogen-activated protein kinase), and programmed cell death (PCD) play critical roles in plant growth and development, stress response, and disease resistance. In this study, we investigated the interaction of BAG, and MAPK as well as their putative role in PCD under either short or long-term heat stress. We constructed mutants of bag2 and mapk2 in tomato using CRISPR/Cas9. Our results revealed that tomato BAG2 and MAPK2 interacted positively both in vivo and in vitro. In addition, after 3 h of heat stress, the activities of Caspase 3 and antioxidant enzymes, expression levels of Caspase 3 and Caspase 9, and contents of H2O2 in bag2 and mapk2 mutant plants were lower than those in WT (wild type) plants. Moreover, under short-term (3 h) heat stress, the DNA fragmentation phenomena and trypan blue coloration in both mutants were less severe than in WT plants; however, DNA integrities were broken, and the number of dead cells was higher under long-term (24 h) heat stress. Additionally, the electrolyte leakage was increased, but the Fv/Fm (maximum photochemical efficiency) value was decreased in mutants following exposure to heat stress. These results suggested that tomato BAG2 and MAPK2 suppressed short-time heat-induced PCD while promoting long-time heat-induced PCD.