The bomber drove a jeep right inside the packed St Rita's Church, in the Malali area of the city, a volatile ethnically and religiously mixed city, in the morning.
A spokesman for the National Emergency Management Agency (NEMA) in Kaduna said that five people had been confirmed killed, while 98 people were receiving treatment for wounds at two local hospitals, reports Reuters.
There was no immediate claim of responsibility but Islamist sect Boko Haram has claimed similar attacks in the past and has attacked several churches with bombs and guns since it intensified its campaign against Christians in the past year.
"The heavy explosion also damaged so many buildings around the area," said survivor, Linus Lighthouse, saying he thought there had been two explosions in different parts of the church.
Other witnesses and the police said there was just one bomber. A wall of the church was blasted open and scorched black, with debris lying around. Police later moved in and cordoned the area off.
Shortly after the blast, angry Christian youths took to the streets armed with sticks and knives. A Reuters’ reporter saw two bodies on the roadside lying in pools of blood.
"We killed them and we'll do more," shouted a youth, with blood on his shirt, before police chased him and his cohorts away. Police set up roadblocks and patrols across town in an effort to prevent the violence spreading.
At least 2,800 people have died in fighting since Boko Haram's insurrection began in 2009, according to Human Rights Watch. Most were Muslims in the northeast of the country, where the sect usually targets politicians and security forces.
Another witness to the bombing, Daniel Kazah, a member of the Catholic cadets in the church, said he had seen three bodies on the bloodied church floor in the aftermath.
A spokesman for St Gerard's Catholic Hospital, Sunday John, said the hospital was treating 14 wounded. Another hospital, Garkura, had 84 victims, the NEMA official said.
Many residents rushed indoors, fearing an upsurge in the sectarian killing that has periodically blighted Kaduna. A bomb attack in a church in Kaduna state in June triggered a week of tit-for-tat violence that killed at least 90 people.