According to the PlayStation 4 online user guide, the console will not initially support 3D Blu-ray discs.
As reported by The Sixth Axis, the PlayStation 4 online user guide confirms that 3D Blu-rays will not initially be supported by the console, following a recent move from Microsoft concerning the Xbox One.
This is an odd move from Sony, as the hardware is surely capable of playing 3D Blu-rays, since it supports the relevant HDMI 1.3 standard, as well as the power in the box. The PlayStation 3 console handled 3D Blu-ray playback, so this could be a feature that will be later included to the PS4 as a patch.
The confirmation itself is listed under the Video/TV section of the user guide, along with the previously known fact about the absence of MP3 and CD support, which will be patched in later. The section also gives a list of discs that should not be inserted into the console, so I recommend checking it out, just to be on the safe side. Obviously, it also gives a list of discs that the console actually supports, so go check it out, and you might find out that you can do more with your console than you were expecting.