@Configuration
public class DataSourceConfiguration {

    @Bean
    @ConfigurationProperties(prefix = "first.datasource")
    @Primary
    public DataSourceProperties firstProperties() {
        return new DataSourceProperties();
    }

    @Bean
    @Primary
    public DataSource firstDataSource() {
        return firstProperties().initializeDataSourceBuilder().build();
    }

    @Bean
    @Primary
    public JdbcTemplate firstTemplate() {
        return new JdbcTemplate(firstDataSource());
    }
}

@Configuration
@ConditionalOnProperty(name = "second.datasource.url")
public class SecondDataSourceAutoconfiguration {

    @Bean
    @ConfigurationProperties(prefix = "second.datasource")
    public DataSourceProperties secondProperties() {
        return new DataSourceProperties();
    }

    @Bean
    public DataSource secondDataSource() {
         return secondProperties().initializeDataSourceBuilder().build();
    }

    @Bean
    public JdbcTemplate secondJdbcTemplate(@Qualifier("secondDataSource") DataSource datasource) {
        return new JdbcTemplate(datasource);
    }
}

first:
    datasource:
        url: jdbc:h2:firstdb;DB_CLOSE_ON_EXIT=FALSE
second:
    datasource:
        url: jdbc:h2:seconddb
        platform: h2