Yes! The plugin provides a choice of two ways to discontinue a product in WooCommerce:
Immediately - Change the stock status to 'Discontinued', and it stops being purchasable immediately.
When stock runs out - Alternatively, for products/variations where you are actively managing stock, you can tick a box to automatically discontinue it as soon as the stock level reaches zero. This is the best way to use up your remaining stock before removing the product from sale.