Aspergillus niger F22, which produces oxalic acid (OA) as a nematicidal component, can be used to control root-knot nematodes (RKNs). OA or OA-producing microorganisms are known to induce resistance against plant diseases caused by fungi, bacteria, and viruses, but their effects on RKNs have not yet been elucidated. This study investigated the ability of an A. niger F22 formulation (Nemafree, 20% SC) and OA to induce tomato resistance against Meloidogyne incognita. Foliar-spray and soil-drench treatments of Nemafree and OA effectively controlled M. incognita in laboratory experiments. When Nemafree (4000-fold dilution) and OA (0.22 mM) were applied 4 days before inoculation with M. incognita eggs, they reduced root gall formation by more than 50%. In field experiments, the Nemafree soil drench also effectively reduced root galling. Moreover, the Nemafree and OA treatments enhanced the transcriptional expression of pathogenesis-related 1, proteinase inhibitor-II, and polyphenol oxidase genes and improved the production of total phenols, flavonoids, and lignins in tomato plants infested with M. incognita. These results demonstrate that low concentrations of A. niger F22 formulation (Nemafree, 20% SC) or OA can induce resistance in tomato plants and effectively control RKNs. Accordingly, our study demonstrates that microbial nematicides producing OA as an active component can sustainably control RKNs through both induced resistance and direct nematicidal activity, thereby providing alternatives to chemical treatments and their negative environmental impacts.