The fungal pathogen Fusarium oxysporum f. sp. dianthi (Fod) is the causal agent of the vascular wilt of carnation (Dianthus caryophyllus L.) and the most prevalent pathogen in the areas where this flower is grown. For this reason, the development of new control strategies against Fod in carnation has been continuously encouraged, in particular those based on the implementation of plant resistance inducers that can trigger defensive responses to reduce the disease incidence, even at lower economical and environmental cost. In the present study, the effect of the soil supplementation of a biotic elicitor (i.e., ultrasound-assisted dispersion obtained from Fod mycelium) on disease severity and phenolic-based profiles of roots over two carnation cultivars was evaluated. Results suggest that the tested biotic elicitor, namely, eFod, substantially reduced the progress of vascular wilting in a susceptible cultivar (i.e., ‘Mizuki’) after two independent in vivo tests. The LC-MS-derived semi-quantitative levels of phenolic compounds in roots were also affected by eFod, since particular anthranilate derivatives, conjugated benzoic acids, and glycosylated flavonols were upregulated by elicitation after 144 and 240 h post eFod addition. Our findings indicate that the soil-applied eFod has an effect as a resistance inducer, promoting a disease severity reduction and accumulation of particular phenolic-like compounds.