I assume you use pconnect - otherwise you wouldn't have any opened connections left.
You could use mysql function
KILL thread_id_number
To get list of all running threads use processlist (SHOW PROCESSLIST).
I'm sure there is a mysql function which can do it at once (flush-threads?) but I don't remember it now... or maybe there is not?
To limit the maximum thread timeout (after which the thread is killed and you have again one mysql connection freed) you could use mysql option wait_timeout=value, set in mysql config file or via command line when starting mysql daemon.