Makes no sense. First off, you don’t have a Canon 5D shooting video, you have a 5D Mark II/III and if it’s recording H.264 (it is) Apple should love it. You don’t mention what operating system you were using before Yosemite, but if you have a 2013 (new cylinder) Mac Pro it was Mavericks.
I reply because I come from a 13″ 2010 MacBook Pro (Snow Leopard was great) left it with good ol’ Mountain Lion and went to Yosemite with my new (2014) 15″ MacBook Pro: and iffy FCP7. So now I use Adobe, hoping to learn Avid. But no problems seeing the cards from my old T2i, mounts like any other drive ( same old DCIM files). Make sure you have the latest firmware updates for the camera
https://www.usa.canon.com/cusa/support/consumer/eos_slr_camera_systems/eos_digital_slr_cameras/eos_5d_mark_iii#DriversAndSoftware
and the latest Apple Pro Video Formats update (current version 2.0.2) via App Store: that should be it. Still have to convert it from the camera to ProRes to edit, but if you’re shooting people (low on action), it still looks great (even on a 40ft screen). Hope this helps some, but it should be working regardless.
p.s. This site is BIG on precise, applicable information of your system, answers are slower with less…ml