Abadi issued "an order to relieve the Baghdad Operations commander of his position, and relieving security and intelligence officials in Baghdad of their positions," a statement said.
The head of the Baghdad Operations Command was Lieutenant General Abdulamir al-Shimmari, but the premier's office did not identify the other officials who were removed.
A suicide bomber detonated an explosives-laden minibus in a Baghdad shopping district early on Sunday as it teemed with people ahead of the holiday marking the end of the holy month of Ramadan.
The blast, which was claimed by the Islamic State jihadist group, killed 292 people, making it one of the deadliest ever bombings by militants in the country.
The initial blast killed a limited number of people, but raging flames spread and trapped people inside shopping centres at the site that lacked emergency exits, police Major General Talib Khalil Rahi said.
Interior Minister Mohammed Ghabban tendered his resignation following the bombing, and authorities also announced the execution of five convicts and the arrest of 40 jihadists in an apparent bid to limit the fallout from the attack.
Ghabban criticised the security system as fundamentally flawed, saying he could no longer accept responsibility for the consequences and calling for a series of changes that would ultimately increase the ministry's power.
An official in Abadi's office told AFP on Wednesday that the premier had accepted the minister's resignation, though there has been no official statement from him on the matter.
IS overran large areas north and west of Baghdad in 2014, but Iraqi forces have since regained significant territory from the jihadists.
In response to the battlefield setbacks, the extremist group has hit back against civilians, and experts have warned there may be more bombings as the jihadists continue to lose ground.
