Certainly, you can configure your product using our Variants feature:
In the case you describe, you would only create variant-configuration lines for the particular color-size combinations you actually have for that product.
When you Add or Edit the product in Seller Admin and enable the "Variants having individual price/weight/stock/SKU" setting for that product, on the next screen you can name up to three Options (you will specify only two, named Size and Color), then below that provide a list of every possible combination you will offer, following our standard format of:
(Note here I happened to give every combination the same price and weight, but you can make them different if you wish, and I gave each one a different amount of in-stock inventory units, if you wanted to enable Inventory Control in the cart to avoid selling a sold-out combination. :^)