Gqozo stood up and turned to look at the massacre victims and their families seated in the first three rows of the 800-strong audience before telling them: "Please forgive me. I know that I do not deserve your forgiveness.
"I want to tell you from my heart that I never wanted your people to be killed. I will not be surprised if you reject my (apology). You have lost loved ones."
Twenty-nine people were killed when Ciskei Defence Force troops opened fire on African National Congress marchers gathered near Bisho Stadium on September 7, 1992.
The mother of the only Ciskei soldier to die on the day of the shootings began wailing loudly as Gqozo told the commission he doubted ballistic evidence which suggested the soldier was killed by a fellow CDF member.
She was escorted out of the hall by commission officials and sedated.
Questioned on the involvement of the then South African government in the events which led to the massacre, Gqozo said he rejected suggestions that he had been a puppet "of the whites used against blacks".
"I owed no allegiance to the Pretoria government. On the contrary I had a lot of fights with them. They definitely did not like me. I did not condone apartheid. I would never have done anything they said I should do."
Gqozo was also questioned on his continued insistence that CDF troops acted defensively in opening fire on the ANC marchers.
"I don't think they would have shot if they were not feeling threatened," he said.
The commission heard evidence earlier this week which suggested the CDF troops panicked when they were confronted by a group of marchers moving towards them.
Eastern Cape commission head Bongani Finca told a media briefing that Gqozo would be subpoenaed by the commission to appear at an in camera hearing "which will give us more time to probe".
He described Gqozo's submission as "very disappointing", saying he had divulged no new information.
Gqozo was to have addressed a media briefing after giving his evidence, but made a hurried departure after concerns were raised about the presence of a group of protesters at the city hall entrance.
Finca said there were fears that the group could try to block off the front and rear entrances to the hall, posing a security risk to Gqozo.