Mr Zaeef is the best known public face of the Taleban
The US has also announced that it has taken into custody one of the highest-ranking members of Osama Bin Laden's al-Qaeda network, Ibn Al-Shaykh al-Libi, who reportedly ran training camps for the group.
But the Taleban's leader, Mullah Mohammad Omar, has escaped from his hideout in southern Afghanistan on a motorbike, according to an Afghan official.
US military officials indicated that Mullah Zaeef had been taken on board the USS Bataan in the Arabian sea for interrogation.
Asylum denied
Mullah Zaeef is thought to be the most senior Taleban official among the 307 currently held by the American military on the Bataan and in the Afghan city of Kandahar.
It is not clear whether the Pakistan authorities delivered him directly into the hands of US forces.
Pakistani Foreign Ministry spokesman Aziz Ahmed Khan would only say: "He crossed the border into Afghanistan as far as the Government of Pakistan is concerned."
Mullah Zaeef became the best-known public face of the Taleban during the US-led campaign in Afghanistan, giving regular news conferences broadcast around the world.
He was detained in Islamabad on Thursday. and taken to Peshawar for questioning.
Mullah Zaeef, who is 34, provided a line of communication with his isolated and reclusive leaders.
He used his Islamabad news conferences to lambaste the American-led campaign until the Pakistani authorities ordered him to stop making political points.
His two wives and six children are still reported to be in Islamabad.
Omar uncertainty
An intelligence official in Kandahar told the AFP news agency that Mullah Mohammed Omar had slipped past anti-Taleban forces in Helmand Province, where he had been holding out in Baghran district.
"We know where Mullah Omar is. But... we cannot disclose it for the time being," the official said.
Mullah Omar was reported to have left Baghran by motorcycle with four of his supporters.
Afghan foreign ministry spokesman Omar Samad said that the Taleban leader would be "captured dead or alive".
"We don't care if he's on a motorbike, a bike or a donkey." said Mr Samad. "He needs to be arrested and brought to justice."
The surrender of Taleban sympathisers in Baghran, who were able to go free after handing over their weapons, was brokered during the last few days in negotiations with local tribal leaders.
Our correspondent says their submission appears to indicate the weakness of the remnants of the Taleban movement in the country.
Developments in Germany
The German authorities, meanwhile, say they have arrested a suspected member Osama Bin Laden's network in a raid on a hotel in the western city of Moenchengladbach.
Officials said the man, who has an Italian name, was unarmed. He was charged with membership of an illegal organisation.
Since the attacks in New York and Washington in September - which the US blames on Bin Laden's network - German police have been conducting an investigation throughout the country. Three of the hijackers had lived in the northern city of Hamburg.
Earlier police in Bremen searched the apartments of a Lebanese and a Tunisian suspected of membership of an illegal organisation, although no arrests were made, officials said.