The scandal-hit institution also announced today that when it merges with Trinity Saint David and Swansea Metropolitan University, it will come together under the former’s charter, not that of the University of Wales.
There have been calls from Welsh vice-chancellors for the institution to be wound up after a BBC investigation uncovered a visa scam at a linked college.
The Quality Assurance Agency has also found failings in the university’s scrutiny of international partners.
However, D. Hugh Thomas, chair of the university’s council, said that he had stepped down as a result of the decision over the charter, and not because of a call by Leighton Andrews, the Welsh education secretary, for him to consider his position.
“The historic decision taken by the governing body – during my chairmanship – has caused me to assess what in leadership terms is in the best interests of the transformed university,” he said.
The decision over the charter was made in the “context of the objectives set by the Welsh government”, a statement from the university says.
Medwin Hughes, the University of Wales' vice-chancellor, said: “I warmly welcome the historic decision taken today by the University of Wales council. The transformed university will serve and deliver for Wales.
“Our country will have several universities which can all be regarded as national institutions, each one delivering to their core strengths and specific mission.
“After a decade of leading academic institutions, I look forward to working with the government and other institutions in Wales to establish a strong higher education sector.”
He added: “Wales needs strong brands, and the University of Wales has committed itself to an irreversible change which will deliver for our nation; it signifies a sense of history but also a commitment to a new beginning."