It seems you've done this through XML, but if you were working in new Spring best practice, your config would be in Java, and you could exclude them as so:
@Configuration
@EnableWebMvc
@ComponentScan(basePackages = "net.example.tool",
excludeFilters = {@ComponentScan.Filter(
type = FilterType.ASSIGNABLE_TYPE,
value = {JPAConfiguration.class, SecurityConfig.class})
})