The testimony from the last prosecution witnesses wrapped up the first stage of the trial, which began more than a year ago.
The defendant, Tiny Virginia Makopo, allegedly tried to kiss and fondle the victims and is also accused of assaulting one of the girls as well as fellow supervisor. The 28-year-old pleaded innocent to 14 charges of indecent assault, assault and criminal injury.
Makopo's lawyer is expected to start the defense stage Monday. A verdict could be months away.
Much of the evidence so far has come from students who testified in a closed session because of their age.
The scandal erupted at Winfrey's $40 million school outside Johannesburg soon after it opened in 2007 amid great fanfare. The Chicago-based media mogul has spoken out about being sexually abused as a young girl, and she was devastated by the allegations.
Ifunanya Maduka, dean of students at the academy, told the court Tuesday about how one girl told her that Makopo was in a relationship with one of the students.
The girl recounted an incident when she had walked into Makopo's room and found the matron in an embrace with a girl.
"She said they were touching each other in a way that when they saw her they jumped apart," Maduka said.
Another girl broke down and confided in Maduka that Makopo had tried to "throttle" her during an argument.
"She described Tiny as getting angry, pushing her and putting her hands around her neck," Maduka said.
Makopo's lawyer Mosala Mmoleli told the court that his client denies the incidents took place, but Maduka said she did not believe the girls were lying.
"After I reported it, other girls came forward," she said. "I don't know if so many girls can make up the same things."
Maduka, who at the time was coordinator of extracurricular activities for students, said she had to remove Makopo as one of the sports coaches after girls complained she was too "aggressive."
Maduka also said that Promise Mweli, the dorm matron Makopo allegedly assaulted, was "terrified" of Makopo.
Maduka testified that the then head of the academy, Nomvuyo Mzamane, favored the dorm matrons over other staff and would penalize anyone who criticized them. This made students scared of speaking out, Maduka said.
Mzamane, who was dismissed after the allegations surfaced, is suing over remarks Winfrey made at the time.
On Monday, Mweli, who shared a room with Makopo, testified that she would fly into violent rages. She recounted two arguments where Makopo had physically and verbally assaulted her.
In one incident, she came across Makopo in a classroom with the girl she had allegedly been embracing.
Makopo was "yelling and throwing things on the floor." She also threatened to "kill anyone" who tried to take the girl "away" from her, Mweli said.
Mweli, who is no longer working at the school, also told the court that the girl would write letters to Makopo, slipping them under the door of the matron's room.
On Wednesday, Indhira Naik, the former head of security at the academy, testified that Makopo had refused to cooperate with her investigation into the altercations between her and Mweli.