Kakashi wins. He has 6paths chakra, so he should be able to touch the truth seeking balls(Obito did when he absorbed it on Madara). Not to mention kamui can warp them. With 2 MS, it doubles the speed and according to Kakashi, with 6paths power, it's even much stronger. So he can easily render Jubito defensely.
He also showed the capacity to react to the fastest Kaguya ever, so Jubito is never blitzing him, not to mention he has a perfect susanoo defense upgraded by 6paths chakra as well. With intangibility, he can phase through everything Jubito throws at him, and may even manage to simply snipe him in the other dimension judging by the drastical difference in speed(he managed to forcibly close Kaguya's portal before the offensive bone went through it completely).
Kamui shurikens even allows him distance/surprise warpings on anything that make contacts with them. If not, Kamui-Raikiri should be able to seal the deal