Dont forget Madara has one Rinnegan in his socket. He most likly used Shinra Tensei to hold Sasuke in place as he was descending then pickup up his sword as it fell to the ground and impaled him with it.
OT: I don't think he gave Sasuke a Mokuton clone. After all that is a Mokuton tech. you can't learn Mokuton. You need hashi's DNA for it. Now unless Hashirama also supplied Sasuke with Senju DNA I feel the most likely course is Sasuke will awaken the Rinnegan and The whatever the tailed beast planned with Gaara will take effect soon putting both Naruto and Sasuke back on the field to face Madara.