The participation of benzoate (BA), gallate (GA), and salicylate (SA) in various biochemical and physiological processes in plants under conditions of excessive boron (EB) is largely unknown to date. Here, the relationships between phenolic acids (PAs) and the regulation of redox-enzymes, the ultrastructure of cells, and boron forms in the mitigation of EB-induced oxidative stress within tomato calli were studied. Tomato calli were exposed to 2 mM boron (B) in the presence or absence of three concentrations of benzoate, gallate, and salicylate. The data showed that different concentrations of PA counteracted the inhibition of growth and oxidative stress of EB stress by reducing hydrogen peroxide (H2O2) production, lipoxygenase (LOX) activity, boron accumulation forms, cell wall thickening, and moderate concentrations were the most effective. Applications of PAs reduced the catalytic impacts of EB on superoxide dismutase (SOD) and catalase (CAT) activity. Likewise, benzoate and gallate increased the influences of EB stimulation on peroxidase (POD) and ascorbate peroxidase (APX) activities; whereas, SA reduced these effects on both enzymes. PA treatments enhanced the insignificant catalytic effect of EB on the activity of phenylalanine ammonia-lyase (PAL), as well as the stimulation of the negative influence of EB on polyphenol oxidase (PPO) activity. The findings highlight that PAs play an important role in alleviating EB stress in tomato plants by regulating redox enzymes, B-accumulation forms, and cell wall thickening. This study provides new perspectives for strategies related to excess boron tolerance in tomato plants and thus can be used as plant growth promoters.