As Jamie said
A benchmark is a mark, or standard to which we compare our efforts. Maybe once it was a mark in a bench or timber board.
A yard stick is a stick/timber pole which is one yard long (i.e. 91.5 cm long). Think of it as a stick to measure something - the length of a field or building.
In your question you note that they are sometimes can mean the same thing, but Jamie above points out how they are different. A benchmark is a mark to which we compare ourselves/our efforts. A yardstick is the tool by which we measure something also, but in a sense of length, rather than quality. But similar too.