I recently published a project that allows PHP to obtain and interact with a real Bash shell. Get it here: https://github.com/merlinthemagic/MTS
You can get a real bash shell as root. You can then either trigger your php script or execute the commands directly in bash.
After downloading you would simply use the following code:
$shell = \MTS\Factories::getDevices()->getLocalHost()->getShell('bash', true);
$return1 = $shell->exeCmd('yourFirstCommand');
$return2 = $shell->exeCmd('yourSecondCommand');
//the return will be a string containing the return of the script
echo $return1;
echo $return2;
//or if you want to trigger your script as root
$return3 = $shell->exeCmd('php /my/script.php');
echo $return3;
//If your script contains code to make an SSH connection to another server
//there is a much easier way to do that using the project:
$shell = \MTS\Factories::getDevices()->getRemoteHost('ip_address')->getShellBySsh('username', 'secretPassword');