I had the same problem using Tomcat7 with mysql-connector-java-5.1.26 that I put in both my $CATALINA_HOME/lib and WEB-INF/lib, just in case. But it wouldn't find it until I used either one of these two statements before getting the connection:
DriverManager.registerDriver(new com.mysql.jdbc.Driver ());
OR
Class.forName("com.mysql.jdbc.Driver");
I then followed up with removing mysql-connector-java-5.1.26 from $CATALINA_HOME/lib and the connection still works.