404 Error in Joomla 3.8 when .htaccess is enabled - php

Question

I enabled Use URL Rewriting in the Joomla backend and renamed htaccess.txt to .htaccess using the terminal. I'm on AWS Ubuntu 16.04 currently. I have mod_rewrite installed.
Only my homepage works. The rest of the pages give a 404 error. How do i sort this out?
Here's my .htaccess file if anyone wants to see:
##
# #package Joomla
# #copyright Copyright (C) 2005 - 2017 Open Source Matters. All rights reserved.
# #license GNU General Public License version 2 or later; see LICENSE.txt
##
##
# READ THIS COMPLETELY IF YOU CHOOSE TO USE THIS FILE!
#
# The line 'Options +FollowSymLinks' may cause problems with some server configurations.
# It is required for the use of mod_rewrite, but it may have already been set by your
# server administrator in a way that disallows changing it in this .htaccess file.
# If using it causes your site to produce an error, comment it out (add # to the
# beginning of the line), reload your site in your browser and test your sef urls. If
# they work, then it has been set by your server administrator and you do not need to
# set it here.
##
## No directory listings
<IfModule autoindex>
IndexIgnore *
</IfModule>
## Can be commented out if causes errors, see notes above.
Options +FollowSymlinks
Options -Indexes
## Mod_rewrite in use.
RewriteEngine On
## Begin - Rewrite rules to block out some common exploits.
# If you experience problems on your site then comment out the operations listed
# below by adding a # to the beginning of the line.
# This attempts to block the most common type of exploit `attempts` on Joomla!
#
# Block any script trying to base64_encode data within the URL.
RewriteCond %{QUERY_STRING} base64_encode[^(]*\([^)]*\) [OR]
# Block any script that includes a <script> tag in URL.
RewriteCond %{QUERY_STRING} (<|%3C)([^s]*s)+cript.*(>|%3E) [NC,OR]
# Block any script trying to set a PHP GLOBALS variable via URL.
RewriteCond %{QUERY_STRING} GLOBALS(=|\[|\%[0-9A-Z]{0,2}) [OR]
# Block any script trying to modify a _REQUEST variable via URL.
RewriteCond %{QUERY_STRING} _REQUEST(=|\[|\%[0-9A-Z]{0,2})
# Return 403 Forbidden header and show the content of the root home page
RewriteRule .* index.php [F]
#
## End - Rewrite rules to block out some common exploits.
## Begin - Custom redirects
#
# If you need to redirect some pages, or set a canonical non-www to
# www redirect (or vice versa), place that code here. Ensure those
# redirects use the correct RewriteRule syntax and the [R=301,L] flags.
#
## End - Custom redirects
##
# Uncomment the following line if your webserver's URL
# is not directly related to physical file paths.
# Update Your Joomla! Directory (just / for root).
##
#RewriteBase /
## Begin - Joomla! core SEF Section.
#
RewriteRule .* - [E=HTTP_AUTHORIZATION:%{HTTP:Authorization}]
#
# If the requested path and file is not /index.php and the request
# has not already been internally rewritten to the index.php script
RewriteCond %{REQUEST_URI} !^/index\.php
# and the requested path and file doesn't directly match a physical file
RewriteCond %{REQUEST_FILENAME} !-f
# and the requested path and file doesn't directly match a physical folder
RewriteCond %{REQUEST_FILENAME} !-d
# internally rewrite the request to the index.php script
RewriteRule .* index.php [L]
#
## End - Joomla! core SEF Section.
I have already tried commenting/uncommenting:
Options -Indexes
RewriteBase /

Answer 1

Apparently, I have to edit the 000-default.conf file as well. Here's what I did that solved my problem:
I open /etc/apache2/sites-available/000-default.conf and added this code, restarted apache and it worked like a charm.
<Directory /var/www/html/>
Options FollowSymLinks
AllowOverride All
Order allow,deny
allow from all
</Directory>
Hope this helps someone looking for answers.

Answer 2

Just to add to #Elain's answerr,
Check if you are loading your site over SSL. And if yes, then you have the culprit.
Step 1. edit the virtualhost related to your website but the ssl version (generally its named similar to non ssl version with just the -ssl appended to the name.
Step 2. Put the following inside the above file.
<Directory /var/www/html/>
Options FollowSymLinks
AllowOverride All
Order allow,deny
allow from all
</Directory>
Step 3.
Disable the config using sudo a2dissite mysite.com-ssl.conf
Step 4.
Enable the config using sudo a2ensite mysite.com-ssl.conf
Step 5.
Restart the apache server, sudo service apache2 restart