Itachi did something to/for him right before he died. You have to "kill the person closest to you" or "your best friend" depending on which translation you like from a long, long time ago. Perhaps the death of Itachi was the push Sasuke needed or maybe Itachi somehow transferred his chakra into Sasuke's head with that one last flick. Still not confirmed. We have been told that the ONLY way to make M.Sharingan not cause blindness is if it's not your own eyes (Madara has his brother's eyes) and there has been no confirmation that there was a surgery while Sasuke was out.
Maybe Itachi figured out a way around it, we don't know. There's been no confirmation that Sasuke's eyes are permanent, there has been evidence that they aren't (they've had chapters of his vision being fuzzy).