This study investigated the ability of aqueous leaf extracts of Heliotropium bacciferum (HE), Ocimum dhofarense (OE), and Zataria multiflora (ZE) to detoxify aflatoxin B1 (AFB1) under in vitro and in vivo conditions. The results showed that HE, OE, and ZE degraded 95%, 93%, and 92% of AFB1, respectively, after 72 h incubation at 37 °C. The degradation of AFB1 was validated by liquid chromatography–mass spectrometry analysis. A molecular ion peak at m/z 313 specific to AFB1 (C17H12O6) was observed in the mass spectrum of untreated AFB1 (control). However, the level of AFB1 was decreased to untraceable levels in response to treatment with these plant extracts. HE, OE, and ZE effectively detoxified AFB1 in a concentration-dependent manner, resulting in mortality rates of 65, 70, and 75% of brine shrimp, respectively, in contrast to 90% in the untreated AFB1 (control). The hepatoprotective effect of HE, OE, and ZE against AFB1-induced oxidative stress pathogenesis was investigated using mice as an experimental model. Glutathione depletion, impairment of total antioxidant capacity, and increase in DNA oxidative damage were observed in liver tissues of mice treated with AFB1. However, HE, OE, and ZE extract supplementation suppressed the oxidative damage associated with AFB1 treatment. Our findings indicated that HE, OE, and ZE were highly effective in the detoxification of AFB1. In addition, HE, OE, and ZE act as potent antioxidants and combat the AFB1-associated oxidative stress and liver pathogenesis, suggesting that these plants might be valuable for the development of functional foods aimed at minimizing the toxic effects of AFB1.