Despite the massive presence of troops aimed at thwarting insurgent attacks in the city, rebels killed two people in a car bomb attack, and clashes also erupted between gunmen and Iraqi forces.
The extra support came as US President George W Bush urged world leaders to boost support for the fledgling government.
The security plan, Operation Forward Together, was the biggest in recent months and Prime Minister Nuri al-Maliki called upon all political groups, religious leaders and Iraqis to support it.
The stringent measure came after Al-Qaeda warned of huge attacks to avenge last week's death of its leader Abu Musab al-Zarqawi in a US air raid and also a day after an unannounced visit by Mr Bush to Baghdad.
Mr Maliki said the "sole objective of these security measures is to protect the lives of people" and he emphasized that no single community was being focused on more than another.
Upbeat from his surprise Baghdad visit, Mr Bush told reporters in Washington that 26,000 Iraqi soldiers, 23,000 Iraqi police officers and 7,200 US-led coalition forces were part of the operation in Baghdad.
Focus on high risk areas
The aim was to "restore security and return law to high-risk areas in the capital city," he said.
"Baghdad is a city of more than 6.5 million residents, and we have got to recognise it's going to take time for these operations to take hold," Mr Bush said.
All the sectarian and ethnic groups in Iraq are represented in the Baghdad province, home to a quarter of the country's population and one of its most unstable regions.
There were traffic jams throughout the city as commuters waited in long lines in front of checkpoints that stopped most cars instead of waving people through as before.
"In spite of all this mess, we hope this security plan will make us safe from car bombs," said Aqil Mohammed Obeid, a minibus driver who had just spent the last hour stuck in traffic. "We support this plan because we just want to live in safety."
Defence Minister Abdel Qader Mohammed Jassim declined to offer details of the operation to reporters, but said in "this operation we have timetable dates and it will build in strength."
Mr Jassim said the operation kept in mind that "what is going is random killing, with 80 percent of violence against innocent civilians, 15 percent against Iraqi forces and five percent against coalition forces."
Checkpoints were being manned by different branches of the security services, with some handled by the police, some by the commandos or national police and others by the Iraqi army.
Officers at the checkpoints were stopping drivers and checking their cars, registration documents and identity papers.
The plan also included house-to-house searches of areas suspected of hiding insurgents as well as a crackdown on civilians carrying weapons - a tall order in militia-run Baghdad neighbourhoods like Sadr City.
In fact, residents of that Shiite neighbourhood of over two million said that no checkpoints had been set up inside their district, but only on the outskirts.
"If they want to make this plan work, they should go after the Shiite areas that have the dangerous militias," said Adel Hussein, a Sunni, as he read a newspaper outside a barber shop in central Baghdad.
Curfew extended
The night time curfew was also extended by two and a half hours and a vehicle ban was announced during afternoon prayer hours on Friday.
Rebels however killed two people and wounded seven in a car bomb attack targeting a police patrol in Baghdad's northern Al-Qahira neighbourhood.
Also Baghdad's Sunni bastion of Aadhamiyah saw clashes between gunmen and Iraqi security forces, but no casualties were reported. Elsewhere in Iraq six people were killed.
In a bid to curb violence in the country Mr Maliki expressed his desire to hold dialogues with rebel groups.
"If their (rebels) hands are not stained with blood we will open the door to them for a dialogue," he said.
Meanwhile, President Bush said that leaders in Europe, Asia and the Middle East will be pressed to support Iraq's fledgling government.
He said that of the 13 billion dollars pledged at a Madrid donors' conference for Iraq, only about three billion had been sent, adding he would "encourage those who have made a pledge to pay up."
Italy began a reduction of its troop strength in Iraq, which will be down to 1,600 men by the end of June, military spokesman Colonel Roberto Tomsi said.
The whole of the Italian contingent, once the fourth largest in Iraq with
3,200 troops, will be pulled out by the end of the year in line with a pledge by new prime minister Romano Prodi.