How did graduate schools come into existence? When did universities start to segregate their certifications into undergraduate degrees (bachelors) graduate programs (master's and doctorates)?  More importantly, why did this separation occur?  What prompted the need for separate levels of certification in academic settings?
Bachelor, master, doctor degrees are medieval European in origin. Wiki has a reasonable page on medieval universities. The primary need for these levels was the certification of who was allowed to teach and what they were allowed to teach in the university. The Catholic Church in the Middle Ages being what it was was concerned with proper teaching to avoid passing along heresies (which universities got accused of from almost the beginning of their existence) which meant you needed a license to teach and to preach in those days.