Fungal pathogens cause extensive plant diseases that damage crop production in the agricultural industry, resulting in annual crop loss, diminished food security, and historically significant epidemics. Though effective fungicides are available, their risks to the environment and animal health have increased the demand for more sustainable methods to control fungal pathogens. In plants, polygalacturonic-inhibiting proteins (PGIPs) play critical roles for resistance to fungal disease by inhibiting the pectin-depolymerizing activity of endopolygalacturonases (PGs), one type of enzyme secreted by pathogens that compromise plant cell walls and leave the plant susceptible to disease. Here, the interactions between PGIPs from Phaseolus vulgaris (PvPGIP1 and PvPGIP2) and PGs from Aspergillus niger (AnPG2), Botrytis cinerea (BcPG1, BcPG2), and Fusarium moniliforme (FmPG3) were reconstituted through a yeast two hybrid (Y2H) system to investigate the inhibition efficiency of various PvPGIP1 and 2 truncations and mutants. We found that tPvPGIP2_5-8, which contains LRR5 to LRR8 and is of only one-third the size of the full-length peptide, exhibits the same level of interactions with AnPG and BcPGs as the full length PvPGIP2 via Y2H. The inhibitory activities of tPvPGIP2_5-8 on the growth of A. niger were then examined and confirmed on pectin agar. Application of both full length PvPGIP2 and tPvPGIP2_5-8 clearly slows down the growth of A. niger and B. cinerea in the presence of pectin. The investigation on the sequence-function correlation of PvPGIP2 suggests that LRR5 could have the most essential structural feature for the inhibitory activities, and may be a possible target for the future engineering of PGIP with enhanced activity. This work highlights the potential of using plant-derived PGIPs as an exogenously applied fungal control agent both to plants and postharvest crops while minimally impacting the environment and human health.