Body putty for seams

You can get 3M firm set seam sealer in a tube that you use with a caulk gun. It will shrink and crack if applied too heavily. A brushable seam sealer in a can works well too. It tends to be a little creamier and easy to spread. You'll find either at an automotive paint supplier or online.

You'll get the best protection by laying down a coat of epoxy primer before applying the seam sealer. That way, if the sealer were to fail, you'd still have a barrier against rust underneath. But the factory didn't do that so...