N.L.
My daughter totally did this when she was about 20 months old. She did it almost absentmindedly. We ended up going for the "multiple barriers" method (band aid, tuck shirt in/full length pjs, extra shirt on top). Even if she wasn't scratching at it, she was touching it or rubbing it. We also gave her a "substitute" to rub/scratch.
Put some ointment on it to help it heal, and try to keep him away from it. :) Easier said than done, I know.