Tomatoes can easily be affected by soft rot, one of the main postharvest infections caused by a bacterium called Pectobacterium carotovorum. This study examined the soft rot control effectiveness by Bacillus amyloliquefaciens in tomatoes, and identify the underlying action mechanisms from the perspective of the inhibition effects of antibacterial metabolites derived from B. amyloliquefaciens on pathogen and the influences of this antagonist on reactive oxygen species (ROS) scavenging capability of the fruit. The results demonstrated that B. amyloliquefaciens effectively lessened postharvest soft rot occurrence in tomatoes. The non-volatile metabolites synthesized by B. amyloliquefaciens suppressed P. carotovorum subsp. brasiliense (Pcb) growth in vitro and in vivo. The antibacterial ingredients presented in methanol-soluble sediments obtained from non-volatile metabolites. UHPLC-ESI-MS spectra revealed that the primary antibacterial ingredients were C12-C15 surfactin analogues, along with C14-C16 iturins and C16-C17 fengycins. Moreover, B. amyloliquefaciens could raise the activity of enzymatic ROS scavenging system in tomatoes, including several antioxidases and the enzymes related to glutathione peroxidase (GPX) and ascorbate-glutathione (AsA-GSH) cycles. In addition, B. amyloliquefaciens increased the levels of non-enzymatic system for ROS scavenging, including AsA and GSH. Together, O2-·production rate, H2O2 and malondialdehyde (MDA) levels were reduced. It suggested that B. amyloliquefaciens enhanced the ROS scavenging ability of tomatoes, thereby improving their resistance to the pathogen.