Value of CLI running php --ini
Configuration File (php.ini) Path: /usr/local/lib Loaded Configuration File: /usr/local/lib/php.ini
Value of phpinfo from my nginx/php-fpm web server page:
Loaded Configuration File /etc/php.ini
So my issue is that the web server php is not loading the MySQL extension causing MySQL not to work. The CLI php is though (proper php.ini is /usr/local/lib/php.ini).