Tomatoes are a nutritious climacteric fruit, but they have a short shelf life and are susceptible to fungal pathogens such as Alternaria alternata, resulting in significant postharvest losses. Chemical fungicides have been traditionally used to manage these issues, but due to health risks and contamination concerns, alternative strategies are needed. Thus, the present research work was conducted to assess the potential of Fagonia indica (FI) and Allium sativum (AS) plant extracts on shelf life and Alternaria alternata disease of tomato fruit during storage. Tomato fruits was treated with 10 and 20% concentrations of these plant extracts kept at ambient conditions (25 ± 2 °C and 70–75% R/H) for 20 days. Various parameters were analyzed, including weight loss, soluble solids concentration, phenolic contents, titratable acidity, disease severity, incidence, mycelium growth, spore germination, and ascorbic acid. The study found that using 20% FI or AS plant extracts significantly inhibited mycelium growth, spore germination, disease incidence, and severity as compared to the control fruit. It also effectively maintained the quality of tomato fruits by reducing weight loss, color changes, soluble solids concentration, and ion leakage. Additionally, it helps retain higher levels of titratable acidity, firmness, ascorbic acid, total phenolic content, and sensory attributes. This suggests that FI and AS plant extracts could be used as an eco-friendly and cost-effective method to inhibit Alternaria alternate diseases and extend the shelf life of tomato fruits.