Among the heavy metal pollutants, Cr (VI) is very toxic to plants because of its mobile nature. Silicon (Si) is a metalloid and is reported to ease the negative effects of heavy metal stress in plants. Thus, the current study was conducted to examine the influence of chromium (Cr) toxicity and the mitigating role of silicon (Si) in tomato plants. Chromium toxicity induced high accumulation of Cr in roots and shoots, thereby decreasing plant growth and biomass yield. Silicon supplementation enhanced the afore-mentioned parameters except Cr accumulation. Silicon also enhanced the translocation factor, total chlorophyll, Fv/Fm, ΦPSII, Φexc and qp but at the same time it decreased NPQ in Cr-stressed plants. The gaseous exchange and relative water content (LRWC) of leaf were improved by Si, that were initially decreased by Cr noxiousness. Malondialdehyde (MDA), hydrogen peroxide, (H2O2) and electrolyte leakage (EL) increased with Cr toxicity, but were reduced with Si application. Cr toxicity boosts the enzyme concentration, and Si supplementation thereafter increased the activities of the enzymes as well as metabolite cycle (Asc–Glu). Chromium stress increased methylglyoxal (MG) by 116.87%, which was reduced by Si supplementation. Silicon increased GlyI (EC: 4.4.1.5) and GlyII (EC: 3.1.2.6) thereby making the glyoxalase system more active for providing tolerance to tomato plants. In conclusion, Cr toxicity triggers detrimental effect on plant growth and physio-biochemical processes. However, Si supplementation reversed partially the Cr toxicity by modulating the levels of osmoprotectants, antioxidant enzyme activities, Asc–Glu cycle and the glyoxalase system.