Actually, no.
After killing a Dragon Soul boss you get a token you can trade for a Crystalline Geode (http://ptr.wowhead.com/item=78890) which can contain (uncut) common, (uncut) rare and the new (uncut) epic gems.
In one of the first comments you'll also find the links to the other 2 types of geodes you can get/buy, but so far on the PTR I was only able to buy the Crystalline ones after clearing normal modes (Madness of Deathwing didn't drop anything so can't tell if it drops a special token to buy one of the others).