Alternaria alternata and Botrytis cinerea are among the primary fungal pathogens of fruits, causing black spot and gray mold disease, respectively. They cause serious losses in yield as well as affect fruit quality. Controlling fruit postharvest diseases largely relies on the use of chemical fungicides. However, the overuse of fungicides makes the produce unsafe due to their residual effects on the environment and human health. Therefore, significant advancements are necessary to investigate and find sustainable ways to prevent postharvest disease of fruits and minimize postharvest losses. This review summarizes the recent developments in the application of biological control and other sustainable approaches in managing fruit postharvest diseases, with an emphasis on A. alternata and B. cinerea, respectively. Furthermore, several action mechanisms, challenges, and prospects for the application of biological control agents (BCAs) are also discussed. Biological control application has been proven to successfully reduce postharvest disease of fruits caused by A. alternata and B. cinerea. In recent years, it has gradually changed from being primarily an independent field to a more crucial part of integrated pest management. Due to their characteristics that are safe, eco-friendly, and non-toxic, several BCAs have also been developed and commercialized. Therefore, biological control has the potential to be a promising approach to replace the use of chemical fungicides in controlling postharvest disease of fruits.