Another "which" question
Solution 1:
The way I read it, which refers to the whole phrase: not the leaf, nor the properties and vitamins, but to the assertion that green tea contains these things. Admittedly, it's a little ambiguous.
I have seem examples where there would be a noun or noun-phrase after the which to clarify the writer's meaning:
Green tea contains the vitamins and healthy properties of the green tea leaf, which fact makes green tea popular among health-conscious people.
Or that could be rewritten as
... green tea leaf, a fact which ...
Solution 2:
I believe it refers to the entire clause, or you could think of it as an implied noun:
Green tea contains the vitamins and healthy properties of the green tea leaf, (a fact) which makes it popular.