Using class-based configuration and annotations it is possible to split the configuration of each Spring Data JPA repository and its respective DataSource in a separate configuration file.
This article have an example: 
@Configuration
@EnableTransactionManagement
@EnableJpaRepositories(
        entityManagerFactoryRef = "barEntityManagerFactory", 
        transactionManagerRef = "barTransactionManager",
        basePackages = { "com.sctrcd.multidsdemo.integration.repositories.bar" })
public class BarConfig {
    @Autowired JpaVendorAdapter jpaVendorAdapter;
    @Bean(name = "barDataSource")
    public DataSource dataSource() {
        return new EmbeddedDatabaseBuilder()
                .setName("bardb").setType(EmbeddedDatabaseType.HSQL).build();
    }
    @Bean(name = "barEntityManager")
    public EntityManager entityManager() {
        return entityManagerFactory().createEntityManager();
    }
    ...
}
Then you’d do the same to FooConfig, that is, for the other configuration class that will set another DataSource, EntityManager and @EnableJpaRepositories.
Via XML the process would be identical. The important thing is that the EntityManager and the TransactionManager especificados em cada configuração de repositório apontem para oDatasource` desired.
							
							
						 
I have been through the same difficulty as you, however my case was to connect in two different relational banks (oracle and postgre) with each one with its entities. I did a lot of research, but I didn’t find anything either. I opened a question in the English OS and I got no answer. So I had to abandon this solution, but still want to know if this is possible with Spring Data.
– humungs
I believe this is possible using a configuration similar to this https://gist.github.com/efraimcf/0af2cc68bfcdfbde55be I have read about some situations where they configured differently, as in this thread: http://stackoverflow.com/questions/13877734/hibernate-using-two-Different-database-schemas-in-the-same-application
– Efraim Ferreira
I made this configuration. But how would you specify which EM the Spring Data Daos would use using the XML configuration?
– humungs
In Hibernate it is already configured by Sessionfactory property packagesToScan ... With JPA, I believe the answer indicated by @utluiz below is the most appropriate
– Efraim Ferreira