Jersey zoo in the UK I think has the atmosphere, picturesque surroundings, the history, the story and the species which is a recipe which make it what I would call beautiful.
In terms of beauty in a grander more historic and aesthetic sense though from some of the pictures I've seen in the gallery many of the German / Austrian zoos (Vienna comes to mind) have beautiful turn of the last century Art Noveau architecture / buildings. I haven't been to any of these though to see them.
I would say that Jardin des Plantes in Paris is another one that like the German examples I mentioned above has that historic stateliness and beauty. I have been to this zoo and personally I found it to be very beautiful and particularly with the surrounding gardens and of course the museums which give it that majestic feel as part of the bigger narrative of natural history and science.