Short Answer: Yes, Yandex does acknowledge and respect the rel=”nofollow” link attribute, and has done since 2010.
It is also a reason as to why some links may not be displayed within the External Links section of YWMT, and is partially the reason as to why the world discovered this change had been made (Webmasters publicly posted in forums having noticed a sharp reduction in links within YWMT).
There was also an update made to this Webmaster help page, which has since been deprecated:
