But hundreds of thousands of pilgrims - defying the attacks - remain in the Iraqi capital for Thursday's culmination of the religious festival.
A 30-year-old Sunni resident of Adhamiya said he was drinking tea and watching pilgrims walk by when he and his friends heard the blast.
"We heard a big explosion and everybody rushed to the site to see bodies and hear wounded people, screaming for help," Saif al-Azami told the Associated Press news agency.
Wednesday's attack took place near the bridge where 900 people died in 2005 in a stampede sparked by a rumour that a suicide bomber was about to strike.
"In this vacuum there are groups which are trying to throw back Iraq to the period of sectarian conflict and to maintain this kind of tension"
Edmund Ghareeb, professor of Middle East studies at the American University in Washington
Earlier on Wednesday, police said an improvised explosive device [IED] had exploded in Baghdad's southeastern Jadida district, followed by another one in Futhaliya district, in the east of the city, killing five Shia Muslim pilgrims and wounding 36 others.
Major-General Qassim Atta, a Baghdad security spokesman, told the AFP news agency that special safety measures, including road closures, were in place to protect the worshippers.
"We continue to organise transport for pilgrims and air surveillance for their benefit," he said.
"The movement of motorcycles, bicycles and carts is banned throughout the city until further notice," Atta said.
Edmund Ghareeb, a professor of Middle East studies at the American University in Washington, said "there's an effort to stir sectarian conflict ... and to use and exploit the vacuum which exists as a result of the inability of the Iraqi politicians to form a new government".
"So in this vacuum there are groups which are trying to throw back Iraq to the period of sectarian conflict and to maintain this kind of tension," he told Al Jazeera.
"And it is in many ways, I would believe, a reflection of the continuing problems which are facing Iraq, particularly the security situation."
Security officials said 200,000 police and soldiers were assigned to protect the pilgrims as they headed to the Musa Kadhim shrine.
Hundreds of tents have been erected to feed people as they pour into the city for the event, which reaches a climax on Wednesday night and early Thursday.
Scott Petersen, a correspondent with the Christian Science Monitor in Baghdad, told Al Jazeera that in the past "these very large Shia pilgrimages have been targeted by Sunni militants interested in increasing sectarian tension" in the area.
The mausoleum has previously been targeted by bombers.
In April 2009, two female suicide bombers detonated their payloads near the shrine, killing 65 people, including 20 Iranian pilgrims, and wounding 120 others.
Iraq has been without a new government since the March 7 election, which produced no clear winner.
Earlier this week, Joe Biden, the US vice-president, met senior Iraqi officials in Baghdad to urge them to select new leaders without further delays.