How Do I Deactivate Just One Product Variant?

In order to deactivate one product variant you will want to set the inventory to 0 and policy as "don't sell". This will remove the product variant from your website. The product variant will still show up on your POS, however when the variant is selected an error message will pop up advising the staff the item is out of stock.

To set your inventory to 0 and update the policy on the product you can go to Store>Inventory. 

For more information on How to Change Inventory Policy: 
https://documentation.commerce7.com/how-to-change-inventory-policy

For more information on How to Adjust Inventory: