Is application to graduate school asking for period of study, or period from beginning study to graduation date?
The form might phrase it this way to allow for differences in national education systems. Not all PhD programmes work on a cohort system where people start and finish at the same time. For example, I did my PhD in the UK and my revisions to the thesis were accepted in December 2011, so I was allowed to carry the title effective December 22; but there are only two graduation ceremonies each year and so I graduated in February 2012.

In answer to your specific question: Where data entry allows comments, I would go for Study start to Study end and manually ad a graduation date. For fixed fields, I would probably go with the date on your certificate as this would cause the least confusion.