Sindisiwe Manqele, 26, claims she killed Mr Habedi in self-defence at his home in Alexandra, Johannesburg.
The first witness, Luyanda Sulupha, told the court how he had tried to revive the 38-year-old star after he was stabbed in the heart.
Mr Habedi was a member of the award-winning group Skwatta Kamp.
The prosecution opened its case in the Randburg High Court by calling Mr Sulupha, a cousin of the deceased who was at home on the night Mr Habedi died in March.
He testified that he had heard the two arguing for some time, beforeshe emerged from their room crying and asking for help.
Mr Sulupha told the court that Ms Manqele told him she had stabbed her boyfriend by mistake but did not elaborate.
During her bail application earlier this year, the suspect showed what she claimed were defence wounds on her stomach and wrists.
However, prosecutors say they can prove that Ms Manqele's wounds were self-inflicted and that she killed the 38-year old unlawfully - allegations she has denied.
An emotional Mr Sulupha broke down when he was asked to look at  a photograph taken by the police of Mr Habedi's bloodied body - the court sitting adjourned briefly to allow him to compose himself.
In court, Ms Manqele, a former economics student at a college in Dublin, Ireland sat next to friends and family.
She covered her face with a scarf throughout the proceedings.
Ms Manqele is out on bail of $720 (Â£470).
The former girlfriend of South African hip-hop star Nkululeko Habedi, known as Flabba, has pleaded not guilty to his murder.