Sunnis also came under attack, as mortars were launched at the Adhamiya district of Baghdad, killing at least 17 people, a police source said.
Ashura ceremonies have been targeted by Sunni fighters in the past.
Suicide bombings and other attacks on Ashura crowds in Karbala and Baghdad in March 2004 killed 171 people.
Iraqi authorities had deployed 11,000 police and soldiers in the city of Karbala, the focus of the Ashura commemoration that marks the death in battle of Imam Hussein, the Prophet Mohammad’s grandson, 1,300 years ago.
His death in AD 680 entrenched the schism between Shia and Sunni Muslims, a split that now continues to divide Iraq.
Hundreds of Shia flayed themselves with chains or sliced the front of their scalps with swords and knives during the commemorations to express remorse and guilt for not saving Hussein.
Dressed in white and with blood streaming from their heads and backs, men of all ages walked towards the tomb of Imam Hussein in Karbala from dawn.
“This is the least we can do for Imam Hussein who sacrificed himself and his family to save the real religion,” said Ali Mohammed, who had cut his head with a sword.
“We do not feel pain. In fact we feel we are one with Imam Hussein.”