If it's a small amount for something like postage you can do it from your Paypal account. Log into your Paypal account and find the payment on the summary page. Click on it and you'll see the "Refund this payment" link. Click on that and on the next page change the amount to what you want to refund, click on Continue and then submit.
If it's more than that and you'd like the ebay fee reduced you can cancel the current transaction (via More Actions, far right of item on your sold page > Buyer asked to cancel). That will automatically refund payment. Then relist at lower price for buyer to buy again. Obviously tell buyer what you're doing first.
