Mkhwebane said her investigation had found that the apartheid government breached the constitution by supplying Bankorp, which was acquired by Absa in 1992, with a series of bailouts from 1985 to 1995.
She also said the government and the Reserve Bank had failed in their role.
Public Protector Busisiwe Mkhwebane in January reopened a probe of Absa, a unit of Barclays Africa, following a wider report published last November by her predecessor.
The government "improperly failed" to implement the Ciex report after commissioning and paying for it.
On Sunday, DA MP and justice spokesperson Glynnis Breytenbach said that with the flurry of reports uncovering state capture, it was more important than ever for the public protector to investigate and report without fear or favour.
Mkhwebane said the changes in the final report were made as a result of responses from parties who were implicated in the report - including the treasury, the presidency, the Reserve Bank and Absa. The price was R1.23 billion and was paid directly to Bankorp shareholders which is why Absa should not be expected to pay again.More news: US college student released by North Korea home, but in coma
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According to the report, Madonsela uncovered corrupt activities involved in the Gupta state capture saga, and recommended that a judicial inquisition of enquiry be set up to investigate the matter.
The Institute for Accountability in Southern Africa (IFAISA) says Absa should pay back the over R1 billion bailout as ordered by the Public Protector's office.
She wants the Constitution to be amended to ensure that the mandate of the Bank promotes economic growth and not only protects the value of the rand exchange rate.
South African bonds weakened on Monday afternoon in line with the rand, which in turn, was affected by local political concerns.
Section 224 deals with the primary object of the South African Reserve Bank.