Musharraf was arrested overnight at his home on the outskirts of Islamabad, BBC quoted police officer Mohammed Khalid as saying. His home in the Chak Shahzad area on the outskirts of Islamabad was declared a sub-jail.
He said the former president was presented before a judge at Islamabad District Court.
TV images showed a bespectacled Musharraf, wearing a sleeveless jacket, being escorted by police personnel.
Musharraf Thursday fled from the Islamabad High Court after it had ordered his arrest. He had gone back to his farmhouse where the police later stood guard, triggering uncertainty.
The Islamabad High Court Thursday dismissed Musharraf's interim bail extension plea and ordered his arrest in the case related to the detention of senior judges.
After his arrest, Musharraf's sprawling farmhouse here was declared a sub-jail.
Dawn, however, said that Musharraf surrendered to the police. He appeared in the court of a judicial magistrate in Islamabad after which he left for his farmhouse.
The court ordered a two-day-long transit remand and he has been directed to appear before an anti-terrorist court within two days' time.
Thursday saw Musharraf escaping from the Islamabad High Court after the court ordered his arrest.
He fled the court premises in a black, bullet-proof SUV with tinted glasses. Escorted by his bodyguards, Musharraf zoomed out of the court premises as security personnel looked on.
The former army chief and president, who had returned to Pakistan last month after four years of self-imposed exile, later reached his farmhouse in Chak Shahzad.
The case was based on an FIR against the retired general registered in Aug 11, 2009 on the complaint of Chaudhry Mohammad Aslam Ghumman, an advocate.
He had asked the police to initiate legal proceedings against Musharraf for detaining over 60 judges, including Chief Justice Iftikhar Muhammad Chaudhry, after proclamation of a state of emergency in the country Nov 3, 2007.
Xinhua recalled that the judges had refused to take oath under a provisional constitutional order initiated by Musharraf.
A lower court had previously issued arrest warrant for Musharraf as he failed to appear before the court despite several orders.
He faces other legal cases, including treason charges for imposing emergency rule, the 2007 assassination of former premier Benazir Bhutto and the killing of Baloch leader Nawab Akbar Bugti in 2006.
Musharraf, who seized power in a coup in 1999 and resigned in August 2008 to avoid impeachment by the parliament, has denied all the charges and vowed to defend himself in courts.
He returned to Pakistan after over four years of self-imposed exile in Britain and the UAE to lead his All Pakistan Muslim League in the May 11 parliamentary elections. But all four applications to contest the polls, including from Islamabad, have been rejected by the Election Commission.