The type III secretion system (T3SS) is a key virulence determinant in the infection process of Pseudomonas syringae pv. tomato DC3000 (Pst DC3000). Pathogen constructs a type III apparatus to translocate effector proteins into host cells, which have various roles in pathogenesis. 4-Hydroxybenozic acid and vanillic acid were identified from root extract of Sedum middendorffianum to have inhibitory effect on promoter activity of hrpA gene encoding the structural protein of the T3SS apparatus. The phenolic acids at 2.5 mM significantly suppressed the expression of hopP1, hrpA, and hrpL in the hrp/hrc gene cluster without growth retardation of Pst DC3000. Auto-agglutination of Pst DC3000 cells, which is induced by T3SS, was impaired by the treatment of 4-hydroxybenzoic acid and vanillic acid. Additionally, 2.5 mM of each two phenolic acids attenuated disease symptoms including chlorosis surrounding bacterial specks on tomato leaves. Our results suggest that 4-hydroxybenzoic acid and vanillic acid are potential anti-virulence agents suppressing T3SS of Pst DC3000 for the control of bacterial diseases.