Confer is monotransitive: it takes only a direct object, not an indirect object, and the recipient of what is conferred must be expressed with a preposition phrase, usually headed by on or upon, although to and with are found in very old writings.
okThe university conferred a degree on him. BUT NOT
∗ The university conferred him a degree.
Consequently only the direct object, the degree, may stand as the subject of a passive construction.
okA degree was conferred on him by the univesity. BUT NOT
∗ He was conferred a degree by the university.
If you need to make he the subject of a passive construction, you must use another verb such as grant or award:
okHe was granted a degree by the university.
okHe was awarded a degree by the university.
Of course you may make he the subject of an active verb such as earn
okHe earned a degree from the university.
Arrowfar points out that your variant be conferred with has appeared in a number of Irish, Australian and South Asian sources: He was conferred with a degree. The active version is much rarer however; I take this to be an error derived from confusion with the use of confer with in the sense have a discussion with.