To change the open_basedir value when using php in CLI mode (not suPhp), you can do so by going to:
Admin Level → Custom httpd configuration → domain.com
In the top text area, insert this one line:
|?OPEN_BASEDIR_PATH=`HOME`/:/tmp:/usr/local/lib/php/|
which is the default value in the templates. Edit the paths in that line to meet your needs.