http://dev.mysql.com/doc/mysql/en/load-data.html
If the LOCAL keyword is specified, it is interpreted with respect to the client end of the connection:
* If LOCAL is specified, the file is read by the client program on the client host and sent to the server. The file can be given as a full pathname to specify its exact location. If given as a relative pathname, the name is interpreted relative to the directory in which the client program was started.
* If LOCAL is not specified, the file must be located on the server host and is read directly by the server.

[...]

When locating files on the server host, the server uses the following rules:

* If an absolute pathname is given, the server uses the pathname as is.
* If a relative pathname with one or more leading components is given, the server searches for the file relative to the server's data directory.
* If a filename with no leading components is given, the server looks for the file in the database directory of the default database.
Nel tuo caso client e server (tranne particolari configurazioni del server molto improbabili) sono la stessa macchina. Credo che basti passargli il path assoluto del file caricato. Bisognerebbe vedere se il server mysql necessità di particolari permessi di accesso a quel file.

codice:
$sql = "LOAD DATA INFILE '" . $_FILES['nome_del_campo_del_form']['tmp_name'] . "' INTO tabella";
mysql_query($sql);
Se non dovesse funzionare prova con la stessa query con l'aggiunta della parola chiave LOCAL