Aubergine (eggplant) is susceptible to fungal wilts caused by Fusarium oxysporum f. sp. melongenae (Fom) and Verticillium dahliae (Vd). Wild and allied relatives represent a good source of resistance, and introgression lines (ILs) have been obtained through introgression of the Rfo-sa1 locus conferring resistance to Fusarium oxysporum from Solanum aethiopicum into cultivated aubergine. In this work, a deep phenotype characterization was performed according to two parameters: progression of symptoms along the stem and disease severity in leaves. This analysis showed that the Fom-resistant ILs carrying introgression of the Rfo-sa1 locus displayed significantly improved tolerance to Verticillium attack after a preliminary inoculation with F. oxysporum. This positive effect was particularly evident when Verticillium inoculation was performed simultaneously or after Fusarium inoculation. Transcript profiling carried out using a combination of suppression subtractive hybridization (SSH), microarray and qRT-PCR analyses of roots inoculated with selected combinations of fungal pathogens enabled the identification of 164 differentially expressed genes between inoculated and uninoculated plants or between different stages after pathogen infection. Overall, the results highlighted a number of candidate genes putatively involved in early defence responses or signalling pathways activated upon infection of aubergine with either Fom and/or Vd, and thus leading to a broad Rfo-sa1-mediated tolerance against both these wilt pathogens.