Police had earlier said the man was "directly linked" to the investigation of the explosions in the London transportation system -- the first on July 7 caused 56 deaths and a second smaller round two weeks later injured one person.
The man who was slain about 10 a.m. Friday as stunned commuters watched was "challenged and refused to obey police instructions," Police Commissioner Ian Blair said.
The man was identified by police as Jean Charles de Menezes, a 27-year-old Brazilian, described by officers as an electrician on his way to work.
"He was not connected to incidents in central London on 21st July, 2005, in which four explosive devices were partly detonated," a police statement said.
At the same time, police said there was a link between four attackers on July 7 and the men who tried to carry out carbon copy attacks July 21.
Police have appealed to the public for help catching the perpetrators of Thursday's smaller round of explosions on three trains and a bus, and released the photographs of four men suspected of being involved.
The photos, taken from closed-circuit TV cameras, showed a man wearing a dark shirt with New York written across it running through a subway station, another man on the upper level of a double-decker bus, and two other men at separate subway stations.
Police have arrested two people, one of whom was connected to Thursday's explosions. A man was arrested in the south London neighborhood of Stockwell, the same area of the shooting, and detectives were searching a premises there, according to a police statement.
In a Birmingham rail station, police arrested a man and seized at least two suitcases, but it was unclear if the arrest was connected to the bombings. The station was evacuated and cordoned off, police spokesman Will Harpur said, the AP reported.
Two men detained Thursday in connection to the attacks were later released without charge.
An al-Qaida-linked group, Abu Hafs al Masri Brigade, claimed responsibility for both rounds of attacks in statements released on an Islamic Web site, but the authenticity of the claim could not be proved.