Soil salinity is considered a serious problem that limits agricultural productivity. Currently, solutions are being sought to mitigate the negative impact of salt on economically important crops. The aim of the study was to evaluate the effect of foliar application of silicon (Si) on the physiological and epigenetic responses of wheat grown under salt stress conditions. The experiment with wheat seedlings was established in pots with 200 mM NaCl added. After 7 days, foliar fertilizer (200 g L−1 SiO2) was used at concentrations of 0.05, 0.1 and 0.2%. Physiological parameters were measured three times. The addition of salt caused a significant decrease in the values of the measured parameters in plants of all variants. In plants sprayed with Si fertilizer under salinity conditions, a significant increase in CCI and selected gas exchange parameters (PN, Ci, E, gs) and chlorophyll fluorescence (PI, RC/ABS, FV/Fm, Fv/F0) was observed. Si doses of 0.1 and 0.2% showed a better mitigating effect compared to the dose of 0.05%. The observed effect was maintained over time. The results obtained indicate a positive role for foliar silicon fertilization in mitigating salinity stress in wheat. Epigenetic mechanisms play an important role in regulating gene expression in response to stress. Changes in the status of methylation of the 5′CCGG3′ sequence of the nuclear genome of wheat plants exposed to salinity and treated with Si at different doses were determined by the MSAP approach. The obtained results showed a clear alteration of DNA methylation in plants as a response to experimental factors. The methylation changes were silicon dose-dependent. These modifications may suggest a mechanism for plant adaptation under salt stress after silicon application.