Cadmium (Cd), being a highly toxic heavy metal, significantly impacts plant growth and development by altering nutrient uptake and causing oxidative and structural damage, resulting in reduced yield. To combat Cd toxicity and accumulation in wheat, it was hypothesized that co-application of Selenium (Se) and Silicon (Si) can reduce the adverse effect of Cd and regulate Cd resistance while improving Se fortification in wheat. Therefore, this study evaluated the comparative effect of Se and Si on the growth and antioxidant defense systems of wheat plants grown in a hydroponic setup. Briefly, the plants were acclimatized to the hydroponic solution for 1 week and then exposed to 10 µmol Cd. Afterwards, the treatments, including 0.2 mmol Si and 1.5 µmol Se, were applied as a root and foliar application, respectively. Plants supplemented with both Se and Si showed improved biomass and other physiological growth attributes, and this response was associated with improved activity/contents of antioxidants, including glutathione (GSH) content, glutathione reductase (GR), ascorbate peroxidase (APX), and catalase (CAT), with related lowering of hydrogen peroxide, malondialdehyde content, and structural damages. Moreover, by Se + Si supplementation, a decrease in total S levels in plant tissues was observed, whereas an increase in total protein concentration and GSH indicated a different and novel mechanism of Cd tolerance and S homeostasis in the plant. It was observed that Si was more involved in significantly reducing Cd translocation by stabilizing Cd in the root and reducing its content in the soluble fraction in both the root and shoot. Whereas Se was found to play the main role in reducing the oxidative damage caused by Cd, and the effect was more profound in the shoot. In addition, this study also observed a positive correlation between Si and Se for relative uptake, which had not been reported earlier. Our findings show that the Se and Si doses together benefit growth regulation and nutrient uptake; additionally, their combinations support the Cd resistance mechanism in wheat through upregulation of the antioxidant system and control of Cd translocation and subcellular distribution, ultimately contributing to the nutritional quality of wheat produced. Thus, it is concluded that the co-application of Se and Si has improved the nutritional quality while reducing the Cd risk in wheat and therefore needs to be employed as a potential strategy to ensure food safety in a Cd-contaminated environment.