How do I remove index.php from the URL?

I have a project where everything on the website is routed via index.php and the way my app is designed, index.php can be removed from the URL safely. So, /index.php/inbox?from=23 can safely be converted to /inbox?from=23.

I need the rewrite rule (Apache 2.4) for doing so. There is a constraint though - I do not want to do it via .htaccess file, but from the host configuration file (/etc/apache2/sites-available/000-default.conf) only. On my development machine, I have the following:

<IfModule mod_rewrite.c>
	# Rules to serve URLs which point to files directly
	# ----------
	RewriteEngine On
	RewriteBase /
        RewriteCond %{REQUEST_FILENAME} !-f
        RewriteCond %{REQUEST_FILENAME} !-d
        RewriteRule ^(.*)$ index.php/$1 [L]
</IfModule>

But this is not working on the server. (I know that RewriteBase is not allowed in the configuration file itself, but removing it does not work either).

What should I do?