Officials said Mullah Abdul Ghani Baradar and his unnamed comrades had disclosed information about their operations which would help unravel their organisation and lead to more arrests.
Mullah Baradar, who is second only to its supreme leader Mullah Omar, was arrested along with several other militant figures ten days ago, as they were establishing a new Taliban command and training centre in Pakistan's commercial capital.
Senior diplomatic sources said the movement's leadership was targeted as it moved from its base in Quetta, Balochistan, to Karachi.
Major General Athar Abbas, chief spokesman for the Pakistan Army, said it had carried out extensive checks to prove the man they arrested was Mullah Baradar, but declined to give further details of his arrest.
"At the conclusion of detailed identification procedures, it has been confirmed that one of the persons arrested happens to be Mullah Baradar. The place of arrest and operational details cannot be released due to security reasons," he said.
Senior government officials claimed both Mullah Baradar and those arrested with him were giving information they believed would lead to others in the Taliban's new Karachi and Sindh headquarters. They are understood to be in the custody of the country's ISI intelligence agency in the city.
"We're now confident we can bust the whole network they've established in Karachi and Sindh. We're expecting some more arrests in the days to come," a senior military official told The Daily Telegraph.
He said they Taliban leadership had switched from Quetta to Karachi, a city of 16 million people, because it believed they would be harder to detect there.
The timing and motivation behind Mullah Baradar's arrest was the subject of speculation last night amid claims he had been in contact with President Karzai in recent months and was in favour of peace talks.
A spokesman for the Maldives government last night confirmed Taliban figures and Afghan government officials had met for talks on the islands shortly before last month's London Conference. The outcome of the talks is unclear.
Leading Washington-based Pakistan analyst Arif Rafiq suggested Islamabad had finally moved to arrest Mullah Baradar to win favour with the West so it would be able to influence the terms of a any new Afghan settlement following the troop surge. Islamabad wants to ensure it is seen as the guarantor of any deal so that Indian influence is minimised.