The two suspects were detained yesterday near the Pakistan-Afghanistan border in Chaman in Balochistan province and are to be handed to Pakistan's Federal Investigation Agency.
Imran Farooq, a founding member of Karachi's influential Muttahida Qaumi Movement MQM party, was stabbed to death near his home in Edgware, north London, in September 2010.
Scotland Yard had named Moshin Ali Syed, 29, and Muhammad Kashif Khan Kamran, 34, as suspects after records showed they left the UK on the night of the murder.
Syed was detained as he tried to enter Pakistan from Afghanistan, local frontier police said. He was held with another man, Khalid Shamim, but sources quoted in British media claimed that Kamran was also already in the custody of the Pakistan security services.
More From This Section
Detectives have been investigating whether Farooq's murder was linked to his plans to break away from the MQM leadership and launch a new, independent political career.
In a statement, the MQM denied any association with the suspects or involvement in the murder of Farooq and accused the Pakistani government of political victimisation.