If it's a graduation gift, it should be something that will last. After all the point of the gift is to celebrate her finishing her school career and she's only ever going to have one graduation.
Japan does some exceptionally beautiful glass like this:
http://www.beadingtimes.com/artist03...ira34-1big.jpg which you can get in pendants in the price range you're talking about. I found it in a lot of shops in Kobe and in....shiga(?) prefecture where I went to a glass factory. I'd be surprised if you couldn't find it in Tokyo. It would also ship easily.
Otherwise something she could take on with her when she moves out of home for good/starts working full-time. Maybe a high-end print if she likes art, or a really good chef's knife if she likes cooking. My sister got a lamp for her graduation. Lacquer ware is hardy to ship and beautiful. A little box or plate or something might make a good gift as it can be both decorative and practical.
Or you could get something connected to her studies; my cousins studied medicine and architecture respectively; one got a custom stethoscope (sparkly and pink. she works in pediatrics now and the kids love it) and the other got a set of drafting tools with his name on them. I got a set of sushi plates and a dictionary.