You can install the extension through SSH, using composer.
1) change the directory to project root/ folder, and run the following command to install and update the AfterPay module and dependencies:
composer require afterpay/afterpay-module
2) Upgrade and flush Magento cache
php bin/magento setup:upgrade php bin/magento cache:flush
More detailed instructions and release notes can be found here: https://bitbucket.org/afterpay-plugins/afterpay-magento-2
The instructions how to update from an old version of the AfterPay module can be found here.