Of the five nights my husband and I spent in Kyoto (from Australia), we went to Vege Note twice. It is an entirely vegan restaurant, and states so on its menu (it also has a small shop of food products). We got off the South / no.6 exit of Marutamachi station (Karasuma line), which it is very close to, about four stops from Kyoto station on the subway.
There is quite a varied menu of main dishes, but we would highly recommend the set menu A for 2000 yen per person.
It includes about half a dozen small Japanese dishes (which were different the second time we visited), green salad, soup (miso or vegetable - we went for the miso, which was delicious and full of vegetables anyway), bread or rice (we chose the bread, and unexpectedly, it was some of the best bread I've ever had - chewy and slighly toasted) and tea or coffee (soy milk on request). We washed the meal down with beer and (vegan) chocolate cake. Vege Note is closed on Mondays and Tuesdays.