Hi,
In order to achieve that you need to go to /admin/gift_cards/, find the gift card there and press disable at the bottom left. The only thing is that the card will be fully disabled. Originally, card can be used multiple times if it still has a balance.
The other way is to use Shopify POS app. There you may apply gift cards the same way as at online checkout.
By the way if you need to extend standard Shopify gift card functionality there is an app Gift Card Hero which allows to schedule gift card send to a recipient, attach a message, cool animated gift card page and lots of other features. You may find it by the link below: