Last week, a criminal investigation was launched into the leaking of the video.
Gen Tomer-Yerushalmi was put on leave while the inquiry took place.
On Friday, Defence Minister Israel Katz said she would not be allowed to return to her post.
Shortly after that, Gen Tomer-Yerushalmi resigned.
In her resignation letter, she said she took full responsibility for any material that was released to the media from the unit.
“I approved the release of material to the media in an attempt to counter false propaganda against the army’s law enforcement authorities,” she said.
That is a reference to efforts by some right-wing political figures in Israel to claim that the allegations of severe abuse of the Palestinian detainee had been fabricated.
She added: “It is our duty to investigate whenever there is reasonable suspicion of acts of violence against a detainee.”
After her resignation, Katz issued a fierce condemnation of her conduct.
“Anyone who spreads blood libels against IDF troops is unfit to wear the army’s uniform,” he said.
Prime Minister Benjamin Netanyahu echoed his defence minister’s words on Sunday, saying that the incident at Sde Teiman was “perhaps the most severe public relations attack that the State of Israel has experienced since its establishment”.
Hours later, the first reports began appearing in the Israeli media that Gen Tomer-Yerushalmi was missing, sparking fears that a political scandal had taken a turn towards tragedy.
A massive search effort was launched. Several hours later, she was found “safe and in good health” in the coastal area of Herzliya, Israeli police said.
Overnight, a police spokesperson announced that two people had been arrested on suspicion of “leaking and other serious criminal offences” as part of an investigation.
Israeli media reported that the pair were Gen Tomer-Yerushalmi and the former chief military prosecutor, Col Matan Solomosh.