Your CLI is referenced to PHP-CLI binaries. But Apache uses its internal module (libapache2-mod-php) to process PHP scripts. You have to downgrade the version of libapache2-mod-php.
Try with below commands
# Install the old version of libapache-php
sudo apt-get install libapache2-mod-php5
# Disable PHP 5.6 module
sudo a2dismod php5.6
# Enable php 5.3 module
sudo a2enmod php5
# Restart Apache
sudo service apache2 restart