It depends on what your contract says.
Normally your options when the appraisal comes in below the agreed upon purchase price, if your contract has an appraisal contingency, are:
1. The buyer can proceed to purchase using the lower appraised value but still paying the seller the full purchase price (because seller won't budge on the price, etc.). Example if the purchase price is $100k, appraisal comes in at $95k. Buyer can still purchase for $100k, the buyer will just have to bring in the $5k difference plus the % down payment on the $95k appraised value.
2. The buyer & seller agree to a new purchase price, be the appraised value or some other figure. Continuing with the example above, the buyer would propose to seller to lower purchase price to $95k, seller agrees, and new purchase price is $95k and that is what the % down payment is based on.
3. Buyer does not want to purchase at the purchase price, seller does not want to budge on the purchase price, buyer gets to back out of transaction with their earnest money but no refund for any other expenses paid (appraisal, home inspection, etc.).
Unless it states in your purchase contract with the short sale lender that THE APPRAISED VALUE WILL BE THE PURCHASE PRICE, you and your agent are going to have to start doing some negotiating.
Call your real estate agent and loan officer in the morning and go over your options.