I know that this sounds lame, but have you tried restarting your Mac? I had a user that was having problems with some animations on their site. They restarted their Mac and the problems had corrected themselves. This may not be the case in this situation, but it may not hurt to try.
@Elixir
I have two Mac, a MacPro 2013 and a MacPro 2009.
Both updated to El Capitan + Safari 9 and restarted many times in these days.
But I just restarted again… the same, no CSS3 animations in Safari 9.