Firstly check the current configuration
/usr/local/cpanel/bin/rebuild_phpconf --current
Output:
Available handlers: suphp dso cgi none
DEFAULT PHP: 5
PHP4 SAPI: none
PHP5 SAPI: suphp
SUEXEC: enabled
RUID2: not installed
Enable if needed FastCGI by running
/scripts/easyapache
Here is syntax of rebuild_phpconf command
Usage: /usr/local/cpanel/bin/rebuild_phpconf [--dryrun] [--no-restart] [--no-htaccess] [--current|--available] [--errors] <Default PHP> <PHP4 Handler> <PHP5 Handler> <Suexec>
Here is how should look your command
/usr/local/cpanel/bin/rebuild_phpconf 5 none fcgi 1
where,
5 – default php version
none – means you don't need php 4 version
fcgi – php handler
1 – suexec is enable (change to 0 for disabling)
Done, enjoy!