Asif Ali Zardari was released last month from eight years in jail after the supreme court granted him bail involving other cases over alleged corruption.
"Judge Pir Ali Shah cancelled the bail and issued a non-bailable warrant of arrest for Asif Zardari," Zardari's lawyer Shahadat Awan said after the hearing in the southern city of Karachi.
The judge cited Zardari's failure to attend proceedings in the murder trial, said Awan.
Maula Bakhsh Bhatti, a government prosecutor, confirmed the orders to arrest Zardari, saying the court issued non-bailable warrants for the former lawmaker.
The court is carrying out the trial in connection with the killing of a former judge and his son in Karachi eight years ago. Both were shot dead near their home while they were driving in a car.
Details about what allegations Zardari faces in the case were not immediately available.
Bhutto was twice elected prime minister, but in both cases her governments were dismissed over allegations of corruption and misrule in the 1990s.
Zardari is accused of illegally making money while his wife was the prime minister. He has been a member of the senate and was minister for investment in Bhutto's cabinet.
He was scheduled to travel to Rawalpindi, a city near the capital Islamabad, later on Tuesday to address a rally.