The court of Additional Chief Judicial Magistrate, Alipore, gave 28-year-old Shami - now touring West Indies with the Indian cricket team and playing the second and final Test match of the series - 15 days to surrender and apply for bail.
The warrant was issued as the brothers did not appear before the court even once after the hearing started.
After hearing both the prosecution and the defence, ACJM Subrata Mukherjee gave a 15-day window to Shami as he was abroad with the national side. The arrest warrant would remain in abeyance during the next 15 days.
However, if Shami did not surrender to the court during this time frame, the law would take its own course, the judge said.
On the other hand, the court ordered the warrant against Shami's brother to be immediately executed.
The arrest warrant came around six months after the police filed a charge sheet against the celebrated Indian cricketer under Sections 498A (domestic violence) and 354A (sexual harassment) of the Indian Penal Code.
Hasin Jahan had, in 2018, filed a police complaint levelling multiple allegations against the cricketer and four of his family members. The allegations also included rape by Shami's elder brother, attempt to murder and physical assault. However, the police dropped these three allegations while framing the charge sheet.
News of the cricketer's marital discord became public last year, when Hasin Jahan, a former model, took to Facebook to accuse him of domestic violence and extra-marital affairs with a number of women.
Shami, who made his debut for India in 2013, reached the landmark of 150 Test wickets in the ongoing Test match - the 42nd of his career.