Blackleg is an acute and frequently fatal infection that mainly affects cattle and is caused by Clostridium chauvoei. Formalin-killed, whole-cell vaccines are commonly used to control blackleg. The aim of this study was to verify the protective efficacy of two commercial vaccines against the infection of guinea pigs with two strains of C. chauvoei, a virulent field strain (SBP 07/09) and the reference strain used in official tests (Manguinhos-Teixeira or MT). The strains used in the challenge were characterized by whole genome sequencing, and the minimal inhibitory concentrations of 15 antimicrobials were determined. To assess the protective efficacy, guinea pigs were vaccinated and subsequently challenged with C. chauvoei. All four vaccinated and challenged groups seroconverted after vaccination, while the control group remained seronegative, as determined by indirect ELISA. The identical performance of the two C. chauvoei strains in terms of virulence after challenge and their inability to infect vaccinated animals was correlated with their high genetic homology. Both commercial vaccines showed good protective efficacy against both the reference and field strains. Although C. chauvoei vaccination failures have been reported, the results from our study and others reported high similarity among C. chauvoei strains from all over the world, which suggests that the vaccine failures are not due to antigenic variability but inadequate vaccine management.