Intenta alguna solución ya hecha y probada:
Código PHP:
<?php
include 'config.php';
include 'opendb.php';
$tableName = 'mypet';
$backupFile = 'backup/mypet.sql';
$query = "SELECT * INTO OUTFILE '$backupFile' FROM $tableName";
$result = mysql_query($query);
?>
Código PHP:
<?php
include 'config.php';
include 'opendb.php';
$backupFile = $dbname . date("Y-m-d-H-i-s") . '.gz';
$command = "mysqldump --opt -h $dbhost -u $dbuser -p $dbpass $dbname | gzip > $backupFile";
system($command);
?>
Espero que sirva, saludos