You can do this with modifiers for the item in the Square Online Store editor. For example, have size as modifier and color as a modifier, then require the customer to pick one and a maximum of one by clicking the gear icon next to the modifiers. The problem you will run into is there isn't an inventory tracker for modifiers.
If you want to track inventory, a better solution is to you variations named Red-Small, Red-Medium, Blue-Small, etc. Although it is not two dropdown boxes, it will allow you to keep track of your inventory and not sell an out of stock for an item. It would be nice if you could have an extra layer of control here.
