Excess boron (EB) is a known threat to plant growth and productivity, however, the role of applications of phenolic acids [PAs; benzoic acid (BA), gallic acid (GA), and salicylic acid (SA)] in mitigating this threat has not been extensively explored. In vitro investigations were performed to realize the mechanism of PAs on the tolerance index (TI), boron (B) accumulation, and non-enzymatic antioxidants in alleviating EB on tomato (Solanum lycopersicum L. cultivar Castle Rock) calli. Tomato calli were subjected to two levels of B (medium B condition (control) and 2 mM boric acid) in the presence or absence of different concentrations of PAs. The results showed that moderate levels of BA (1.0 μM), GA (10 μM), and SA (50 μM) promoted inhibition of the TI, flavonoids, and ascorbate (AsA) of EB-treated calli. The B concentration was increased under EB, and this parameter was significantly decreased by PAs. Malondialdehyde (MDA), bound phenolics, cysteine (Cys), glutathione (GSH), and protein thiols (PTs) were increased under EB but were significantly reduced through the use of PAs. Free phenolics were increased under EB and were significantly decreased by PAs, only BA increased its content in calli. In addition, EB reduced non-protein thiols (NPTs); however, this deficiency was alleviated by PAs, only SA reduced its content. These results provide new visions to the mechanism that helps control EB in tomato plants and thus can be harnessed to develop effective plant growth stimuli.