I worked around it and there is a programming tweak for sending notification to users for course enrollment.
Create a custom function for send email
require_once("config.php");
require_once($CFG->libdir.'/moodlelib.php');
function custom_send_mail($to_email_id,$sender_email_id,$subject,$title,$body)
{
$mail = get_mailer(); // This will get the moodle mailer configuration.
$mail-> ....
$mail->send();
}
Now all you need to do is find when and where does admin enroll user to the course. I found it here
project_moodle/enrol/manual/ajax.php
Include function in this page
add a line before sending ouput via ajax. (In my case, I added it before echo json_encode($outcome);)
custom_send_mail($user->email,$USER->email,"Project_Moodle Notification","Enrollment Notification","You have been enrolled to course '".$course->fullname."'");
Note: I did this in moodle 2.6 with SMTP configured in moodle.