Have your rule like this:
RewriteCond %{THE_REQUEST} /index\.php [NC]
RewriteRule ^(.*?)index\.php$ /$1 [L,R=301,NC,NE]
RewriteCond %{REQUEST_URI} (\.html?|\.php|/[^.]*)$ [NC]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^ index.php [L]