"We admit here today that something went wrong in the process of gathering the information and reporting" of several top stories, Sunday Times editor Bongani Siqoko wrote in a column.
"What is clear is that we committed mistakes and allowed ourselves to be manipulated by those with ulterior motives... We apologise."
Among the stories was an exclusive published in December 2011 about an alleged rogue police unit accused of scores of extrajudicial killings in the coastal province of KwaZulu-Natal.
The paper said at the time that it had uncovered evidence of a "death squad" operating in the town of Cato Manor on the outskirts of the province's capital Durban.
Dozens of police officers from the top anti-crime unit were arrested and suspended in 2012 in the aftermath of the Sunday Times investigation. While some have been cleared and all eventually allowed back to work, 27 still remain on trial over the claims.
The accused have denied the allegations, arguing they were targeted because they had been investigating high-profile individuals with political ties.
On Sunday, the Sunday Times acknowledged it "failed to present (information) in a prominent way that would have resulted in a balanced and fair piece of journalism that reflected both sides".
Besides the Cato Manor scandal, the paper also admitted that it had falsely reported on an alleged rogue spy unit inside the South African Revenue Service (SARS) in 2014 that surveilled politicians including Zuma.
"While we were interrogating, investigating and reporting these stories, there was clearly a parallel political project aimed at undermining our democratic values and destroying state institutions, and removing individuals who were seen as obstacles to this project," the paper's editor said.
"We admit that our stories may have been used for this purpose."
Siqoko said the paper would return awards won for these stories.
In power since 2009, the corruption-tainted Zuma was forced out of office by his ruling African National Congress (ANC) in February.
His successor Cyril Ramaphosa has promised to turn the page on the political and financial scandals that have engulfed the government.
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