Just when they stab each other there was clear eye contact. Danzo could have used it on Sasuke and make him fight Tobi, right?
Danzo had just used the Kotaamatsukami at the Five Kage Summit, and I believe that the eye needed some time to regain the power, that's why he asks his subordinates to fight Tobi first. Then while fighting Sasuke he uses the other Sharingan (located in his arm)... He basically wanted to use the Kotoamatsukami against Tobi, because he was the main guy to be controlled.
Realistically speaking, Danzo still has to wait until he uses Kotoamatsukami again. But hypothetically, this wouldn't have much of a benefit. First off, during the fight Sasuke spammed the HECK out of his MS' abilities. Tobi even stated it himself. So, if Danzo used Kotoamatsukami, his only hope will be Sasuke's strong visual prowess. Which would probably be on the verge on blindness after a few attacks. Not to mention that Tobi has a way to counter pretty much all of Sasuke's MS abilities. So if he used Kotoamatsukami, it'd be kinda useless and would have to wait another time because he used it to try to kill someone who had no interest in his battle, but only Shisui's eye. Hope my answers reasonable. :)