Phytopathogenic bacteria represent a risk to global food production by impacting a variety of crops. The aim of this study was to characterize the contents of bioactive constituents in extracts from Ginkgo biloba L. leaves and fruits and test their activity against six phytopathogenic bacteria that affect horticultural crops. Gas chromatography–mass spectrometry (GC−MS) was used for the chemical profiling of the aqueous methanol extracts, and their bacteriostatic activity against Clavibacter michiganensis subsp. michiganensis, Pseudomonas cichorii, Pseudomonas syringae pv. pisi, Pseudomonas syringae pv. syringae, Pseudomonas syringae pv. tomato, and Xanthomonas vesicatoria (formerly Xanthomonas campestris pv. vesicatoria) was determined in vitro through the agar dilution method. The protective effect of the leaf extract was tested in vivo against the most relevant bacterial pathogens based on their economic/scientific importance, i.e., C. michiganensis subsp. michiganensis and P. syringae pv. pisi, in tomato (Solanum lycopersicum L.) and pea (Pisum sativum L.) plants, respectively, under greenhouse conditions. The GC−MS characterization of G. biloba extracts revealed the presence of dihydro-4-hydroxy-2(3H)-furanone, 2,4-dimethyl-3-hexanol, catechol, 3-O-methyl-D-fructose, 4,6-di-O-methyl-α-D-galactose, methyl 2-O-methyl-α-D-xylofuranoside, and 3-methyl mannoside. In vitro growth inhibition tests showed that, while the fruit extract had no activity, the leaf extract exhibited minimum inhibitory concentrations between 500 and 1000 μg mL−1, which may be attributed to the presence of 2,4-dimethyl-3-hexanol and catechol. In vivo tests of the leaf extract demonstrated full protection in tomato and pea plants at 1000 and 1500 μg∙mL−1, respectively. The results indicate that G. biloba leaves may be employed as a biorational source for integrated pest management in horticulture.