Scarcity means limitedness, which is used in the context of natural resources, that can be reproduced but still scarce as at a given point of time, the availability is limited.
occurs whenever quantity demanded is greater than quantity supplied at the market price. More people are willing and able to buy the good at the current market price than what is currently available.
The shortage, on the other hand, is a market phenomenon, used for products and services which are not available in the required quantity.
When a shortage exists, the market is not in equilibrium. At equilibrium, the quantity demanded equals the quantity supplied at the market price.
The easiest way to distinguish between the two is that scarcity is a naturally occurring limitation on the resource that cannot be replenished. A shortage is a market condition of a good at a particular price. Over time, the good will be replenished and the shortage condition resolved.