The use of biological plant protection products is promising for agriculture. In particular, chitosan-based biopesticides have become widespread for stimulating growth and protecting plants from a wide range of pathogens. Novochizol is a product obtained by intramolecular cross-linking of linear chitosan molecules and has a globular shape, which provides it with a number of advantages over chitosan. Novochizol has previously been shown to have a stimulating effect on the growth and development of common wheat (Triticum aestivum L.). However, the effect of this preparation on the protective mechanisms against rust diseases has not been studied before. Our studies have revealed the dose effect of the preparation on the development of stem rust of wheat. When treating plants with novochizol at a concentration of 0.125% four days before infection, the best results were obtained, namely: a stable reaction was observed and the number of pustules decreased. To identify critical points of the drug’s effect on the protective mechanism against stem rust, we used an adrenaline test, which allows for a quick assessment of the pro/antioxidant status of plant extracts. We also assessed the activity of the major antioxidant enzymes, peroxidase and catalase, using commercial kits and the Folin–Ciocalteu reaction to assess the concentration of phenolic compounds. As a result, two stages were identified in infected plants pretreated with novochizol: early (up to 10 h after inoculation), characterized by antioxidant activity, and late (10–244 h), with prooxidant activity. These stages correspond to two peaks of accumulation of reactive oxygen species (ROS) in response to pathogen infection. The first peak is associated with the accumulation of superoxide anion O2−, which is converted into oxygen and hydrogen peroxide under the action of the enzyme SOD (superoxide dismutase). The second peak is associated with the accumulation of H2O2. Hydrogen peroxide performs a protective function leading to the death of pathogen mycelial cells. In comparison with infected plants without novochizol treatment, we found a decrease in the activity of catalase (an enzyme that breaks down H2O2) at both stages, as well as peroxidase in the interval from 10 to 144 h after inoculation. Also, an increase in the concentration of phenolic compounds was found in the treated infected plants. We suggest that these changes under the influence of pretreatment with novochizol contribute to enhancements in plant defense functions against stem rust. Taking into account the physicochemical advantages of novochizol over chitosan, which provide a very low effective dose of the drug, the obtained results indicate its promise and safety as a biological plant protection product. This work is a preliminary stage for an extended analysis of the effect of novochizol on plant immunity using biochemical and molecular genetic approaches.