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The name of the new university would be Sefako Makgatho Health Sciences University, Higher education Minister Blade Nzimande said in a statement.
"The university is named after a highly-acclaimed politician, journalist, educationist and theologian.
"We are proud to advance his lifelong struggle for a South Africa that is legitimate, non-racial, non-exploitative, free, independent, democratic, and playing its proper role amongst the nations of the world," Nzimande said.
Sefako Mapogo Makgatho was the second president of the African National Congress.
The new university would be merged with the Medical University of Southern Africa (Medunsa) campus in Garankuwa, Pretoria.
Nzimande announced his intention to separate Medunsa campus from the University of Limpopo in May 2011.
The decision was based on the findings and recommendations of a task team's report, led by Professor William Makgoba and Dr Max Price.
"The task team had been appointed to review the impact of the merger of the Medical University of South Africa (Medunsa) and the University of North, which resulted in the establishment of the University of Limpopo.
"When I made this announcement there was a commitment from the department that we would open the doors for learning of this institution at the beginning of the 2015 academic year."