A police said worshippers were walking to an annexe of the mosque during a condolence ceremony on Friday when the explosives, hidden in a car parked nearby, were detonated.
About 180 people were injured in the blast and authorities urged citizens to donate blood to the hospitals.
The attack came after at least five people were killed and eight injured when three roadside bombs exploded in Sadr City in northeastern Baghdad.
Pilgrims targeted
The blasts struck minibuses carrying Shia Muslims home from a pilgrimage in Iraq's holy city of Karbala.
Hundreds of thousands of pilgrims had flocked to Karbala a day earlier to mark the birth of Imam Mohammed al-Mehdi.
Later on Friday, six people were killed and 30 injured after a car bomb struck a
crowded market in the mixed Sunni-Shia Khadra neighbourhood in western Baghdad.
No group has claimed responsibility for the attacks.
Thursday's Karbala pilgrimage was the second major religious gathering in Iraq since the withdrawal of US troops from urban centres on June 30.
Attacks by al-Qaeda remain common, raising doubts about the Iraqi security forces' ability to stand alone.
On Thursday, a roadside bomb hit pilgrims on their way to Karbala, killing one and wounding four others.
Last week, a string of bombings targeted Shia worshippers in Baghdad during Friday prayers, killing at least 29 people.