Mpembe said he was hurt by statements made by Michelle le Roux for the South African Human Rights Commission during cross-examination on Tuesday.
"Yesterday, there was an insinuation that I am very unhelpful and unco-operative," he said.
"I respect the commission and everyone here … this was reported all over the news last night … I humble myself before the commission," Mpembe said before breaking down in tears.
On Tuesday, Le Roux told the commission that information provided by police was inadequate and the commission would have to rely on one side.
Commission chairman, retired judge Ian Farlam, told Le Roux that was not true, and the commission's report would be balanced.
Le Roux told Mpembe that she did not imply that he was unhelpful.
"I said that because although as overall commander you do not have personal knowledge of the events last year."
Farlam requested a short break to allow Mpembe to recover, after which Le Roux said evidence provided by Mpembe regarding the strike-related unrest has not assisted the commission at all.
"It is important that the commission understand who was in charge," said Le Roux.
"Your evidence has not been able to assist the commission. You do not have personal knowledge despite being the overall commander."
Le Roux said she hoped that other members of the South Africa Police Service due to testify would shed more light on the events at Marikana.
Vuyani Ngalwana, for the police, said Le Roux's statement was "nothing but grandstanding".
"This has no basis at all chairperson … to say that my client has not assisted the commission is just grandstanding."
Commission chairperson, retired judge Ian Farlam, said Le Roux's statement was not helpful.
" … To say evidence has not assisted the commission is certainly not helpful and cannot certainly be put as a fact."
The commission is investigating the deaths of 44 people killed during strike-related unrest at Lonmin's platinum mining operations at Marikana, near Rustenburg in North West, in August last year.
Police shot dead 34 people, almost all striking mineworkers, on August 16 2012, while trying to disperse and disarm them.
Ten people, including two police officers and two security guards, were killed in the preceding week. – Sapa