Brigadier Amir Nayif and his son were shot dead as they left the family home on Monday, a police source said.
Nayif died 10 minutes after he was transferred to al-Yarmuk hospital, Rafi Hamdi, an Iraqi journalist told Aljazeera.
Nayif's son, Lieutenant Khalid, died immediately after being hit by several bullets. Their car crashed into a house after they were shot, the journalist added.
Also on Monday, in southwest Baghdad, a roadside bomb destroyed a US tank, killing two US soldiers and wounding four, the US military said.
The attack raised to at least 1067 the number of US troops killed since the start of the war that toppled Iraqi leader Saddam Hussein in 2003.
Witnesses to the Baghdad deputy police's chief's killing said Brigadier Nayif was not guarded, making himself an easy target for fighters who escaped after the attack
In a separate incident, a number of US soldiers were reportedly killed and others injured when an explosive device hit a US military patrol in Abu Ghraib, west of Baghdad, sources told Aljazeera.
Brigadier Amir Nayif was without
armed guards when he was killed
The US military said on Monday that a marine had been killed in action in al-Anbar province in western Iraq.
In other incidents, Aljazeera has learned, US combat helicopters bombed different sites in the northern city of Mosul on Monday.
US and Iraqi forces also closed five bridges in the city.
In southern Baghdad, a bomber driving a police car blew himself up at a police station, killing at least three Iraqis and injuring many more, a police source said.
He said the powerful blast in the Zaafaraniya area sent a column of black smoke rising into the sky.
Iraq's fledgling security forces have borne the brunt of attacks by fighters who accuse them of collaborating with US-led forces in the country.