Commission chairman Archbishop Desmond Tutu described the document as an "extraordinarily powerful statement", and welcomed it on behalf of the commission and of victims of apartheid.
He said the submission had been endorsed by journalists, in their individual capacities, from Beeld, Die Burger, Rapport, Volksblad, Insig, Huisgenoot, Sarie, You and Fair Lady, as well as a number of former Naspers journalists. More were expected to sign.
"While I understand they are not acting under threat of losing their jobs, I want to commend the journalists warmly for following their consciences in the face of very considerable opposition," Tutu said.
"Theirs is a very significant contribution to reconciliation and the process of healing our land."
The journalists said they were making the submission as individuals, and not on behalf of Naspers or any of its publications.
They said they believed reconciliation between, and the just treatment of, different groups of people in South Africa were essential to nation-building, and that disclosure of the past was an essential part of this.
Since early this century a close relationship had developed between Naspers and the National Party, with Naspers newspapers acting as NP mouthpieces.
They said Naspers newspapers had formed an integral part of the power structure which implemented and maintained apartheid through, for instance, supporting the NP in elections and referendums.
The efforts Naspers had made to change and oppose apartheid should be acknowledged, as should its efforts to persuade and prepare whites for change and reform.
This, however, did not diminish or neutralise support for apartheid.
The journalists said although they had not been personally or directly involved in gross human rights abuses, they regarded themselves as morally co-responsible for what happened in the name of apartheid because they helped maintain a system in which these abuses could occur.
They said they had been blind and deaf to the political aspirations, anger and suffering of their fellow South Africans.
"I, like many others... did not properly inform readers of the injustices of apartheid," each of the 127 said in an individually signed statement.
"(I) did not oppose these injustices vigorously enough and, where I had knowledge of these injustices, too readily accepted the National Party government's denials and reassurances.
"To all those who suffered as a result of this, I offer my sincerest apology and fully commit myself to preventing the past from being repeated."