During the three-month retrial, the jury heard that the trio, all close friends of the bombers, had been key members of a tight circle around ringleader Mohammad Sidique Khan.
All three, the jury was told, shared a violent jihadist ideology.
Prosecutors in both trials had claimed that the men's movements in London mirrored a scouting trip by the bombers and included sites ultimately attacked.
Neil Flewitt QC had told the trial that the case centred on circumstantial evidence which, he argued, created a compelling picture of guilt.
But the trio maintained throughout the trial - and during tense evidence from the witness box - that they ideologically opposed suicide bombings and had been shocked by the attacks.
Counsel for the men told the jury there was no evidence linking them to the bombings and that they were being tried for guilt by association.
Mr Flewitt said a December 2004 trip to London lay at the heart of the case because the three men, accompanied by two of the eventual suicide attackers, had used it to visit a number of possible targets.
The prosecution said the group's movements bore a "striking similarity" to the final targets.
But the men told the jury that the trip had been organised because Waheed Ali was planning to leave the country for militant training in Pakistan.
He and Sadeer Saleem were going to join the future bombers Mohammed Sidique Khan and Shehzad Tanweer, who had already left.
He wanted to say goodbye to his sister, who lived in the capital. The others, the court heard, had simply gone along for the ride.
Ali and the other two defendants had attacked the trials as a witch-hunt, motivated by a determination to see someone pay for the murders.
Trio cleared over 7/7 attacks
The three men acquitted were arrested in 2007 amid the largest criminal investigation yet in the UK. But the 2008 trial reached a stalemate after almost three weeks of deliberations by the first jury.
After Sadeer Saleem's release by the court, his solicitor, Imran Khan, read out a statement on his behalf, in which Mr Saleem supported calls by families of the bombing victims for a public inquiry.
We are not looking for people to blame, but we also know that we have not been told the whole truth
"I must make it absolutely clear that I had nothing whatsoever to do with the dreadful attacks on 7 July 2005, which I have always condemned," he said.
Home Secretary Jacqui Smith said she welcomed the two guilty verdicts.
"It clearly demonstrates the determined stance the UK takes against those suspected of involvement in terrorism," she said.
Graham Foulkes, whose 22-year-old son David was killed in the Edgware Road Tube explosion, has called for a public inquiry into the bombings.
He said: "For almost four years we have been asking for an inquiry into what led up to 7/7.
"We are not looking for people to blame, but we also know that we have not been told the whole truth.
"We believe that crucial lessons need to be learned. If mistakes have been made, they should be put right, not covered up. This is not a witch-hunt, it is simply about saving lives."
Tens of thousands of police hours have been spent on the four-year investigation - and detectives maintain there are people in the Leeds area who know more that could help them.
The defendants accused the police and media of creating a climate of fear in the Beeston area of Leeds, where they live.
Sadeer Saleem's solicitor Imran Khan reads out a statement after the acquittal
West Yorkshire Police assistant chief constable John Parkinson said "intensive scrutiny" from police, public and media had put pressure on the residents of Beeston, and also Dewsbury, where some of the 7/7 bombers lived.
He added: "Local people were very supportive of the investigation, both immediately after the event and in the many months that followed.
"The attacks on 7/7 have shown us that we all need to work together if we are to effectively respond to the threat of terrorism."
Deputy assistant commissioner John McDowall, head of the Metropolitan Police Counter Terrorism Command, called for anyone with information about the attacks to come forward.
"While those directly responsible for the bombings died in the attacks, we remain convinced that others must have been involved in the planning," he said.
This page is best viewed in an up-to-date web browser with style sheets (CSS) enabled. While you will be able to view the content of this page in your current browser, you will not be able to get the full visual experience. Please consider upgrading your browser software or enabling style sheets (CSS) if you are able to do so.