The Islamabad High Court rejected Musharraf's plea for extension of bail in connection with the sacking of over 60 judges during the emergency.
69-year-old Musharraf, who returned to Pakistan on March 24 after a nearly four-year long self-imposed exile abroad to contest the May 11 general elections, appeared in the High Court under a thick security blanket.
Dismissing his application, the bench ordered the police to arrest him immediately.
Soon after the court order, Musharraf's security team quickly rushed him out of the courtroom to his black SUV without being stopped.
Musharraf's motorcade then drove out of the court complex in the presence of a battery of armed security personnel.
TV news channels reported that Musharraf's motorcade drove from the court to his farmhouse at Chak Shahzad on the outskirts of Islamabad.
Musharraf's security team comprises army commandos.
A large number of Musharraf's supporters, gathered at the court complex, scuffled with lawyers, who called on police to implement the High Court's order to arrest the former President.
Since Musharraf's return to Pakistan last month, he has been in and out of court several times to get his bail extended over the 2007 killing of former premier Benazir Bhutto, the death of a Baloch leader Akbar Bugti in a 2006 military operation and for imposing emergency rule in 2007.
The Taliban have also threatened to target him.
Earlier this week, Musharraf was disqualified from contesting next month's general election, effectively ending his ambitions for a political comeback.