Small CD player

47 Labs Shigaraki 4716 (mind you, this is a transport only but the matching DAC is a real dwarf)

Isem eGo

The 47Labs Shigaraki 4715 is indeed very small (3 x 3.15 x 3.15 inches), but you may have to find place for its separate power unit behind the stand or shelf, then
http://www.sakurasystems.com/products/shigadac.html

The same goes for the transport btw.

To get a better idea of sizes, look up Srajan's review on 6moons, there is a picture with the 4 boxes sitting on one shelf

For completeness' sake and in full unawareness of your budget, there is of course also the full-out-assault Nagra CDP (12x10x3).
Still, no SACD, but from the original question I took that this is an annoyance but not necessarily a show-stopper?