In northern Kirkuk, a bomb killed two men heading to a mosque for Ashura.
Police, meanwhile, said security forces ended an uprising by members of the Soldiers of Heaven cult in the two southern Iraq cities of Basra and Nasiriya, which killed at least 70 people.
Pilgrims thronged the streets of Karbala to mark the slaying of Imam Hussein by the armies of the caliph Yazid in AD 680.
Akil al-Khazali, Karbala's governor, told a news conference: "Two million people have come to Karbala for Ashura.
"There have been no security violations ... and the ceremonies have gone ahead without incident," he added, as buses began ferrying the pilgrims home.
Earlier in the week, the governor had announced the deployment of about 20,000 security force members in and around the city for the event.
Drums and trumpets sounded from early morning around the shrines to Imam Hussein and Imam Abbas in Karbala, announcing the start of the day's processions and prayers in the shrine city.
|Iraqi forces ended an uprising by theSoldiers|
of Heaven cult in Basra and Nasiriya [AFP]
Iraqi helicopters circled the city while pilgrims were frisked up to 10 times before they could reach the shrines.
Processions, which began with thousands of devotees drenched in blood after "tatbir", or the ritual of flagellating their scalps, ended with a re-enactment of the battle for Karbala in AD 680 in which the Imam Hussein was killed.
Medics walked through the crowd treating flagellation wounds.
Fighting raged through the afternoon in Nasiriya, about 350km south of the capital Baghdad, and Basra, in southern Iraq, during which officials said police posts and several Ashura processions were attacked by members of the Soldiers of Heaven cult with machineguns and rifles.
Clashes died down in Basra during the night, but continued sporadically in Nasiriya.
Imam Hussein's death entrenched the schism between Shia and Sunni Muslims over who should be recognised as the successors of Prophet Mohammed.