Musharraf, who ruled Pakistan from 1999 to 2008, has been accused of failing to provide adequate security to Bhutto when she returned to Pakistan from exile in 2007, reported Xinhua.
Bhutto, who had twice served as prime minister, was killed in a suicide attack and gunshots in the garrison city of Rawalpindi in 2007, shortly after she addressed thousands of her supporters at an election rally.
Musharraf's government had accused the Pakistani Taliban of killing Bhutto, the charge denied by the Taliban.
The Federal Investigation Agency (FIA), which is investigating Bhutto's murder, had sought Musharraf's custody to question him about his failure to ensure security for the former prime minister despite serious threats to her life.
Musharraf's lawyer Afshan Adil opposed the FIA request and argued that there is no evidence against the former president.
Judge Chaudhry Habib-ur-Rehman of the anti-terrorism court accepted the FIA request and granted Musharraf's five-day physical remand.
The court ordered that Musharraf should be presented again before it April 30.
Several security agencies have constituted a Joint Investigation Team to question Musharraf for the assassination of Benazir Bhutto.
Musharraf will be questioned at his heavily-guarded Islamabad farmhouse, which has officially been declared a sub-jail.
The former president was not shifted to prison on a request from the authorities over threats to his life by the Taliban militants, who in a video message last month announced to launch an attack on Musharraf.
Musharraf, who returned to Pakistan last month after over four years in self-exile, has denied all charges against him and said he would defend himself in courts.
Musharraf has already been arrested in the case of keeping the judges in illegal confinement when he imposed Emergency rule in 2007.
The former president is also facing high treason charges for abrogation of the constitution, that paved the way for declaration of Emergency.
Five people have filed petitions for high treason proceedings in the Supreme Court. However, the interim government has refused to pursue the case because of its limited role. The interim government has prayed to the apex court to leave the case to the next elected government.
Musharraf has floated his own All Pakistan Mulsim League, which is to contest the parliament elections slated for May 11. His own bid to contest the polls has, however, failed as he was disqualified due to criminal cases against him.