ε-Poly-l-lysine (ε-PL) is a natural antimicrobial polymer with significant inhibitory activity against a broad spectrum of microorganisms, and nowadays used widely as a preservative in the food industry. In the present study, ε-PL broth was obtained from Streptomyces ahygroscopicus GIM8 fermentation in a nutrient-limited liquid medium. The in vitro antifungal activity of the broth against fruit pathogens Penicillium expansum and Colletotrichum gloeosporioides was investigated, and its usage for postharvest storage of two highly perishable fruits wax apple and guava was evaluated. Results showed that ε-PL concentration in the broth reached 0.61 g/L, and the nutrition level of the broth was low. The antifungal activity of ε-PL broth was comparable to that of the aqueous solution of ε-PL under the same concentration. Immersion with the diluted broth (200 mg/L ε-PL) markedly delayed the decline in the quality of postharvest wax apple and guava fruits during storage, and the decay incidences were also greatly decreased as compared to their respective controls (distilled water immersion). A further investigation demonstrated that the ε-PL broth immersion induced an increase in the activity of defense-related enzymes peroxidase and polyphenol oxidase in the two fruits during storage. The present study proved that the fermentation broth of ε-PL could be used as a promising alternative to high purity ε-PL and synthetic fungicides for preserving fruits at postharvest stage.