The announcement was made on Thursday evening by the World Trade Center Captive Insurance Company, which was set up to handle the claims of those injured in the rescue effort.
In a statement, New York Mayor Michael Bloomberg called the settlement "a fair and reasonable resolution to a complex set of circumstances".
Some workers are expected to receive payments of only a few thousand dollars, while others could be in line to get more than $1m, depending on their injuries.
The BBC's Adam Brookes, in Washington, says the agreement means that the long-running legal battle spawned by the 9/11 attacks may now be drawing to a close.
The twin towers' fall covered Lower Manhattan in dust and debris
After the twin towers fell on 11 September 2001, rescuers spent weeks amid the smouldering wreckage and choking dust in Lower Manhattan, but few were adequately insured for such work.
The government set up a special insurance company to handle claims if any of them ended up injured or sick.
The claims came flooding in, many for cancer and respiratory illness caused by dust.
By early 2008, according to government documents, nearly 10,000 law suits had been filed against the insurance company.
But only six claims were paid out.
Lawyers for the city had claimed it did its best to provide respiratory equipment for workers, and challenged some claims as being based on flimsy medical evidence.
Marc Bern, a senior partner with the law firm which negotiated the deal, said: "We are gratified that these heroic men and women who performed their duties without consideration of the health implications will finally receive just compensation for their pain and suffering."
It is thought that the long courts battle has depleted the $1bn fund created by Congress to help insure the city, with the legal bill so far running to more than $200m.
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