According to the documentation I see that a partial hot backup of a single database can be done by using the --databases option with innobackupex. However, I am trying to find a way to do a restore of this partial backup on a MySQL 5.1 server without having to stop mysql. Not to mention the datadir would not be empty as it would have other database files present. Based on what I’ve read this does not seem possible as it seems the destination server must be Percona server or at least MySQL 5.6. Is anyone aware of a work around for my particular situation?
Yes, it’s possible with Percona Server or MySQL 5.6. You can check this post for details you may find useful http://www.percona.com/forums/questions-discussions/percona-xtrabackup/12415-xtrabackutp-restore-on-another-server-with-another-db-running-on-the-same-server
Other workaround, if your target database is not huge then you can try mysqldump program to backup specific database tables and then restore on target server.