The newspaper said the March 17 online story and a shorter version in the newspaper on March 19 relied heavily on what turned out to be phony FBI documents. The stories were written by Pulitzer-prize winning staff writer Chuck Philips.
The Times also retracted statements Philips made in two online chats and the newspapers' blog. It did not provide details of the statements.
The shooting triggered a feud between East and West Coast rappers that later led to the killings of Shakur and Notorious B.I.G.
"The Times has since concluded that the FBI reports were fabricated and that some of the other sources relied on including the person Philips previously believed to be the 'confidential source' cited in the FBI reports do not support major elements of the story," the newspaper said.
On March 26, The Times posted an article on its Web site saying the authenticity of the documents and story had been challenged. The next day, the newspaper offered a front-page story that reported it had been the victim of a hoax and apologizing for its error.
In a statement Monday, Times editor Russ Stanton did not address why the newspaper published the retraction in addition to the previous apology.
"The Los Angeles Times has taken this matter very seriously," he said. "The retraction that appears in the paper and on our Web site today, and the previously published apology, speak for themselves."
Times spokeswoman Nancy Sullivan declined to comment further.
A message by left by The Associated Press for Combs' attorney Howard L. Weitzman was not immediately returned.
The documents were part of a $19 million federal suit filed in October in Miami by James Sabatino, who is serving a federal prison sentence for fraud. The lawsuit claimed that Combs failed to pay Sabatino for a recording and video session he arranged with Notorious B.I.G.
The documents purported to be an FBI agent's report of interviews conducted in 2002 of confidential informants linking Sabatino and associates of Combs to the attack on Shakur in New York City.
"The Times now believes that Sabatino had no involvement in the attack and that he never spoke to Combs about it. Any statements or implications suggesting that Combs was given advance knowledge of the assault on Shakur, or played any role in it, are specifically retracted," the newspaper said.
Combs has denied that he had any prior knowledge of or involvement in the robbery and shooting of Shakur. He claimed he had been defamed by the newspaper.
The Associated Press erroneously relied on the documents in a Nov. 14 story about the court case and offered a corrective story on March 28.
FBI spokesman Stephen Kodak told The AP that the documents can't be found in the agency's records and do not appear to be legitimate.
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