Spring Boot JPA - configuring auto reconnect

I assume that boot is configuring the DataSource for you. In this case, and since you are using MySQL, you can add the following to your application.properties up to 1.3

spring.datasource.testOnBorrow=true
spring.datasource.validationQuery=SELECT 1

As djxak noted in the comment, 1.4+ defines specific namespaces for the four connections pools Spring Boot supports: tomcat, hikari, dbcp, dbcp2 (dbcp is deprecated as of 1.5). You need to check which connection pool you are using and check if that feature is supported. The example above was for tomcat so you'd have to write it as follows in 1.4+:

spring.datasource.tomcat.testOnBorrow=true 
spring.datasource.tomcat.validationQuery=SELECT 1

Note that the use of autoReconnect is not recommended:

The use of this feature is not recommended, because it has side effects related to session state and data consistency when applications don't handle SQLExceptions properly, and is only designed to be used when you are unable to configure your application to handle SQLExceptions resulting from dead and stale connections properly.

The above suggestions did not work for me. What really worked was the inclusion of the following lines in the application.properties

spring.datasource.testWhileIdle = true
spring.datasource.timeBetweenEvictionRunsMillis = 3600000
spring.datasource.validationQuery = SELECT 1

You can find the explanation out here

Setting spring.datasource.tomcat.testOnBorrow=true in application.properties didn't work.

Programmatically setting like below worked without any issues.

import org.apache.tomcat.jdbc.pool.DataSource;
import org.apache.tomcat.jdbc.pool.PoolProperties;    

@Bean
public DataSource dataSource() {
    PoolProperties poolProperties = new PoolProperties();
    poolProperties.setUrl(this.properties.getDatabase().getUrl());         
    poolProperties.setUsername(this.properties.getDatabase().getUsername());            
    poolProperties.setPassword(this.properties.getDatabase().getPassword());

    //here it is
    poolProperties.setTestOnBorrow(true);
    poolProperties.setValidationQuery("SELECT 1");

    return new DataSource(poolProperties);
}

I just moved to Spring Boot 1.4 and found these properties were renamed:

spring.datasource.dbcp.test-while-idle=true
spring.datasource.dbcp.time-between-eviction-runs-millis=3600000
spring.datasource.dbcp.validation-query=SELECT 1