The court in Rawalpindi issued the warrant after hearing the arguments of prosecution lawyers.
The Federal Investigation Agency also submitted a detailed charge-sheet that named Musharraf as an accused in the case related to the murder of Bhutto.
The judge subsequently adjourned the case till February 19.
The FIA had earlier this week named Musharraf as an "absconder" for failing to cooperate in the probe into the assassination.
Musharraf, currently living in self-exile in Britain, had refused to cooperate with investigators and answer their questions, prosecutors said.
The detailed charge-sheet said that there was a conspiracy behind Bhutto''s assassination, and that Musharraf allegedly provided slain Tehrik-e-Taliban Pakistan chief Baitullah Mehsud with the opportunity to carry out a suicide attack on Bhutto by failing to provide her adequate security.
A report compiled by the FIA''s investigation team said: "Musharraf was equally responsible for facilitation and abetment of the assassination of Benazir Bhutto through his government and justified failure in providing her the requisite security protection that her status demanded twice.
There was a security lapse."
The FIA has also alleged that two top former police officials, who were recently arrested for alleged negligence in providing security to Bhutto, were acting on the orders of Musharraf.
Musharraf''s spokesman and legal aides have dismissed the charges levelled against him, saying the Pakistan People''s Party-led government was trying to deflect attention from charges of inefficiency and corruption levelled against it.
Bhutto was killed by a suicide bomber shortly after she addressed an election rally in Rawalpindi in December 2007.
The former military ruler has been living out Pakistan since April 2009. Former Pakistani Taliban chief Baitullah Mehsud was killed in a US drone strike in 2009.