Plants have evolved a sophisticated chemical defense network to counteract pathogens, with phenolamides and salicylic acid (SA) playing pivotal roles in the immune response. However, the synergistic regulatory mechanisms of their biosynthesis remain to be explored. Here, we identified a biosynthetic gene cluster on chromosome 2 (BGC2) associated with the biosynthesis of phenolamide and SA, wherein the key component SlEPS1 exhibits dual catalytic functions for the synthesis of phenolamides and SA. Overexpression of the key component SlEPS1 of BGC2 in tomato enhanced resistance to the bacterial pathogen Pst DC3000, whereas knockout plants were more susceptible. Exogenous applications of SA and phenolamides revealed that these two compounds act synergistically to enhance plant resistance. Notably, during tomato domestication, a disease-resistant allele of SlEPS1, SlEPS1^HapB, was subject to negative selection, leading to a reduction in phenolamide and SA levels and compromised disease resistance in modern varieties. Moreover, the SlMYB78 directly regulates the BGC2 gene cluster to enhance phenolamide and SA biosynthesis, modulating resistance to Pst DC3000. Our study employed multi-omics approaches to describe the synergistic regulation of phenolamide and SA biosynthesis, offering new insights into the complexity of plant immune-related metabolism.