Scotland Yard said that the man, who has not yet been identified, "was unconnected to the incidents of Thursday 21 July" and was " probably unconnected" to the July 7 bombings.
Police separately said they have arrested a second man in connection with the attempted attacks in London on Thursday. He was also arrested in Stockwell, where the other man was held yesterday.
Friday's shooting occured when armed police pursued a man in Stockwell, south London, as part of an undercover operation. He ran off when challenged, and they shot him, fearing he was about to detonate a bomb. Later, a man believed to be the Shoreditch bus bomber was arrested in the same area. He was led away wearing a white boiler suit.
The disclosure came as Scotland Yard released photographs of the four suspects, taken from closed-circuit television cameras at the three Underground stations and on a bus where the bombing attempts were made.
All the images showed young men of Asian appearance, and police warned people not to approach any of the men, who are now the targets of the most intense anti-terrorism investigation seen in Britain.
Security sources had confirmed on Friday that the man who was pursued and killed in the morning during an undercover police operation at Stockwell Tube station was thought to be linked to the failed bombers.
The man, whose identity has not been released and who was not believed to be armed or carrying a bomb, was shot five times in the head on the floor of an Underground train. The extent of his connections with the alleged bombers is unclear and his death is expected to renew controversies about killings by police firearms officers. The Metropolitan Police has 31,000 officers and 3,000 are licensed to carry firearms.
The developments came as part of an extensive and fast-moving police inquiry being conducted as Londoners attempted to return to work amid widespread public fear of a further attack. Large parts of the Underground network remain out of action as a result of the attacks on 7 July and on Thursday.
Police have confirmed that the four bombs on Thursday at Oval, Shepherd's Bush and Warren Street stations and on the No 26 bus in Shoreditch had all only partly detonated. One, believed to be on the bus, was a nail-bomb in a rucksack, one of thousands of bags given away by the gym chain Fitness First. The three other bombs were of a similar size and contained similar explosives to the devices used by the four suicide bombers on 7 July, when they killed a total of 56 people, including themselves.
To underline the gravity of the situation, Sir Ian Blair, the Metropolitan Police Commissioner, said Scotland Yard was engaged in "the greatest operational challenge" in its history, with officers facing " previously unknown threats and great danger". But he stressed that the police operation was targeted at criminals and not a particular community.
Assistant Commissioner Andy Hayman said: "At this stage, it is believed the devices consisted of home-made explosives and were contained in dark-coloured bags or rucksacks. It is too early to tell how these were detonated."
The shooting at Stockwell Tube station followed intensive overnight police activity resulting from the "forensic goldmine" of the four unexploded bombs. From this, police obtained three addresses, in Stockwell and Brixton, south London, and at west Kilburn, which were put under observation.
Shortly before 10am, a man left the premises in Stockwell and was followed by surveillance officers. He got on a bus and headed towards the nearby Tube station. Fearing he was going to enter the Tube, officers called in an elite unit of specialist firearms officers to make an armed arrest before he entered the station. At this point, witnesses said, the man vaulted a barrier in the Tube station and ran down the escalators and on to a northbound Northern line train, pursued by police.
Mark Whitby, who was on the train, said he heard people shouting, "Get down, get down!" He described how an "Asian guy" ran on to the train pursued by three plainclothes police officers. "He tripped and was also pushed to the floor and one of the officers shot him five times, " he said.
Although other witnesses said the man was wearing a bulky coat "with wires sticking out of it", there was no indication last night that he had been carrying a bomb.
The shooting led to the area being cordoned off and the temporary closure of the Victoria and Northern lines.
The man arrested in South Lambeth, near Stockwell, was thought to be the son-in-law of an older woman living at an address raided by police. The arrested man's wife and young son were also led away by police, according to residents living in the same block of flats.
David Benn-Hirsch, deputy chairman of the local tenants' association, said the older woman had lived in the flat with her family for many years. He said they were Muslims originally from Ethiopia. He added: "I know them as peaceful neighbours and I'm shocked to hear about what has happened."
In further operations last night, addresses in the Harrow Road area of north-west London and Brixton in south London were raided.
- More about: