The current study aimed at assessing the potential effects of Se applied at three levels (0, 20, and 40 mM) in two methods (soil addition or foliar spraying) on the components of the antioxidant defense system and oxidative stress biomarkers in tomato plant growing under irrigation water deficit (from 100% to 60% of soil field capacity; SFC) during the 2017 and 2018 seasons. The results indicated that reducing irrigation water from 100% to 60% of SFC led to a marked increase in oxidative stress biomarkers (malondialdehyde; MDA, hydrogen peroxide; H2O2, and superoxide; O2 • ), which associated with increased contents and activities of the components (enzymatic and non-enzymatic) of the antioxidant defense system in both seasons. Both 20 and 40 mM Se significantly increased contents and activities of the components of the antioxidant defense system, which were reflected in reduced oxidative stress biomarkers. Compared to foliar spray, better results were obtained with Se application to the soil. The interaction among the three factors; water deficit, Se level, and Se application method was significant. The combination of irrigation at 60% of SFC × 40 mM Se application to soil was preferable, which can be recommended for use to support the endogenous antioxidative defense system in tomato plant cultivated in a dry environment.