Post-harvest fungal diseases result in great environmental, economic, and social impacts due to the loss and disposal of food. In tomato cultivation, alternaria spot stands out, caused by different species of Alternaria sp., with losses in the pre- and post-harvest of fruits. Control is made by spraying synthetic fungicides but essential oils and plant extracts with antifungal activity can be an alternative in controlling post-harvest diseases, especially in fruits and vegetables, with increased safety in the consumption of fresh food by reducing the use of synthetic fungicides. Therefore, this study aimed to evaluate the effectiveness and mode of action of aqueous extracts of cinnamon and cloves and their active ingredients in the in vitro and in vivo control of Alternaria alternata in post-harvest tomato fruit. The extracts were evaluated for their ability to inhibit and/or alter mycelial growth, inhibit spore germination in vitro, and control the disease in tomato fruit. Total inhibition of mycelial growth in vitro of A. alternata was achieved by 5% clove aqueous extract and the combination of cinnamon and clove, at concentrations of 2.5 and 5%. In addition, inhibition of spore germination and control of the fungus in tomato fruit post-harvest were also observed. The antifungal activity of these extracts was attributed to the active ingredient eugenol, contained in higher concentrations in clove extract, and the clove and cinnamon mixture, which resulted in morphological changes in the mycelial growth of the fungus and inhibition of spore germination.