Uh, no offense, but could I suggest maybe looking it up? This is according to the dictionary:
cap·stone n.
1. The top stone of a structure or wall.
2. The crowning achievement or final stroke; the culmination or acme.
I would assume that definition #2 fits the situation you described.
The reason UA is referred to as the capstone is that it was founded in 1831 as the top learning and research institution in the state of Alabama.
http://www.ua.edu/history.html