The carnation (Dianthus caryophyllus L.) stands as a key export important for Colombia, yet its production faces challenges due to vascular wilting triggered by Fusarium oxysporum f. sp. dianthi (Fod). This study examined Fod impact on stomatal resistance, leaf temperature, and dry biomass in carnation plants, alongside its influence on rooted cuttings of two carnation cultivars differing in susceptibility to vascular wilting. Employing a completely randomized design, the resistant cultivar ‘Golem’ and susceptible cultivar ‘Mizuki’, each with four weeks of rooting, were inoculated with Fod, while controls were maintained. Both cultivars exhibited altered leaf temperatures and AUDPC (Area Under Disease Progression Curve) parameters post-inoculation, compared to their controls, indicating leaf temperature’s potential as an early Fod presence indicator. The effects of inoculation with Fod for each cultivar were different for stomatal resistance, associated with the asymptomatic stage of the disease. These findings suggest that the resistant cultivar activates early stomatal closure mechanisms, possibly through hormonal pathways, enhancing its ability to combat the pathogen. Real-time PCR analysis of rga1 and mlp43-like genes indicated the involvement of Abscisic Acid (ABA) and Salicylic Acid (SA) hormonal pathways in cultivar-specific responses post-inoculation, even at early stages. These results highlighted Fod presence before symptom development and their significance for devising early detection strategies and breeding genetically resistant cultivars. This study underscores the intricate interplay between plant-pathogen interactions and hormonal signaling pathways, providing valuable insights for effective disease management and cultivar development in carnation production.