The officers will be charged with assaulting Babar Ahmad as they arrested him during a raid at his home in Tooting, south London.
The four, who were all members of the Metropolitan Police's territorial support group (TSG) at the time, are accused of assault causing actual bodily harm.
They are Pcs Nigel Cowley, 32, Roderick James-Bowen, 39, and Mark Jones, 43, and Detective Constable John Donohue who has since transferred to another unit.
Ahmad, 36, who remains in custody awaiting a decision on whether he can be extradited to the United States, welcomed the news.
He said: "I am pleased that the Crown Prosecution Service (CPS) has decided that a jury will hear the evidence in this case.
"It will now be for the jury to determine whether any police officer should be punished for the assault upon me in December 2003."
Ahmad suffered injuries including heavy bruising to his head, neck, wrists and feet when he was arrested in December 2003.
The computer expert was held on suspicion of supporting and helping to recruit terrorists to fight in Afghanistan and Chechnya through email accounts and websites.
Prosecutors considered a file of evidence on how the injuries were caused in 2004 after an inquiry by the Independent Police Complaints Commission (IPCC).
They found there was insufficient evidence for a conviction but reconsidered the case after Ahmad brought a civil case to the High Court last year.
He was awarded £60,000 damages after the court heard evidence he was assaulted and racially abused by a group of officers.
Commissioner Sir Paul Stephenson admitted he was the victim of violence and the officers were accused of a "serious, gratuitous and prolonged" attack.
He ordered an independent review by retired senior judge Sir Geoffrey Grigson into the handling of the case.
Inquiries into the attack were marked by the loss of key documents, including previous complaints against the officers, and the refusal of some to attend court.
Ahmad has never been charged in Britain, but has been held in Long Lartin prison since 2004 after the United States issued an extradition warrant.
In July the European Court of Human Rights halted the move as it considers whether it will breach his rights by exposing him to life imprisonment without parole.
The CPS decision creates a fresh headache for senior Scotland Yard staff over the role of the TSG wing which has been blighted by controversy.
Campaign groups and one member of the Metropolitan Police Authority (MPA) have called for its role to be reviewed.
Last month prosecutors said TSG officer Pc Simon Harwood will not be prosecuted over the death of Ian Tomlinson.
Mr Tomlinson, 47, died after being struck with a baton and pushed to the ground by Mr Harwood on the fringe of G20 protests on April 1 last year.
Simon Clements, of the Crown Prosecution Service, said there was "sufficient evidence and it is in the public interest" to charge the four officers.
James Welch, of Liberty, said: "Justice must take its course in this case. But, as both the Ian Tomlinson and this case suggest, equally important is that the methods and indeed the very existence of the TSG, with its militaristic approach, are urgently reviewed."
Tooting MP Sadiq Khan, a close friend of Ahmad, said: "I am pleased that the CPS decided to look at this incident again.
"Mr Ahmad's injuries, which he received £60,000 compensation for, show there are serious issues to be examined here surrounding the conduct of the arresting officers.
"It is important that these very serious allegations are properly considered in a criminal court, and that justice is seen to be done."
Green Party politician Jenny Jones, a member of the MPA, said: "We've known for many years that the TSG has needed reform.
"There have been consistent allegations of unnecessary aggression and brutality.
"I, for one, am tired of being assured by senior officers that all force has been 'reasonable' only to find out that it hasn't.
"It's difficult to believe even today that this same situation couldn't happen again. Urgent reform of the TSG is needed."
An MPA spokesman said: "This case has serious implications for policing in London. The allegations have damaged public confidence in the way police officers carry out their duties and Londoners have the right to expect that if found to have acted improperly, officers will be held to account.
"Once the legal process is concluded we will seek to publish and debate the findings of the Met review."
A Met spokesman said tonight it had restricted the duties of the four officers.
"The restrictions will be kept under review pending the conclusion of legal processes," he added.
* The men will appear on bail before City of Westminster magistrates' court on 22 September.
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