We can upgrade Magento 2.x via Command-Line Interface (CLI), but I have to remind again that you should backup all your website files before go ahead.
Upgrade Magento 2.x by command
Please back up your composer.json file before continuing.
The followed command will upgrade composer.json file:
composer require magento/product-community-edition 2.1.2 --no-update
Note: As 2.1.2 means the latest Magento version, so the numbers can be changed accordingly.
The followed command could upgrade the files:
Note: It will ask for repo.magento.com authentication keys. For more information, visit this link.
Then execute the followed commands one by one:
rm -rf var/di var/generation php bin/magento setup:upgrade php bin/magento setup:di:compile php bin/magento cache:clean php bin/magento cache:flush php bin/magento indexer:reindex