3M makes a great marine sealant that works well under the waterline. You can get it at any hardware store or even Wal-Mart in the boat section. It's called 3M5200. It's a calk that takes a few days to set up, but then it is pretty durable. If you can get to the inside it would be best to put a bolt or screw thru the hole with a good sized washer on the outside with the sealant sandwiched between the washer and the hull and a nut on the inside. I would hesitate to use just the sealant in such a stressed area as the bottom of the transom. Maybe go up a size and use a self threading screw with the washer and sealant. Make sure you use stainless steel hardware. The Aluminum Boat and Repair board is a good source of info for these type of question:
http://pagebiz.com/bds/aluminum/repair.html