It took me a little while to find the answer to this. It can be done, but the answer isn’t very intuitive.
In iTunes Connect, select your new application & load the details for it. Click the “Binary Details” link. Once this screen is open, there will be a “Reject this Binary” button on this screen.
I found this within the iTunes Developer guide(Link PDF has only 1 page and no other information) under the Rejecting Your Binary section. Apple really could have made the button more obvious.
Note : Link PDF has only 1 page and no other information