Witnesses said the suicide bomber drove his car into the prominent Church of Christ during morning prayers.
No group has claimed responsibility, but suspicion will fall on the radical Islamist sect Boko Haram.
The attack sparked a riot by Christian youths, with reports that at least two Muslims were killed in the violence.
The two men were dragged off their bikes after being stopped at a roadblock set up by the rioters, police said.
A row of Muslim-owned shops was also burned, an AFP reporter at the scene said.
Earlier, the suicide bomber smashed his car through unmanned gates towards the packed church, killing a woman in the process, witnesses said.
The explosives detonated close to where members of the congregation were attending a Sunday service, killing a father and his child.
At least 38 people had to be taken to hospital for treatment, the National Emergency Management Agency said.
The attack sparked immediate anger among Christian youths in the city.
They “were very angry and mobilized… and I overheard them saying they were going to avenge the attack,” one witness was quoted by the APF as saying.
Ethnic and religious tensions run high in Jos, the capital of Plateau state. Hundreds of people have died in bouts of sectarian clashes over the last few years.
But Christian human rights activists suspect Boko Haram of carrying out Sunday’s attack, which they say is the deadliest on a church in Jos.
The group has carried out a number of bloody attacks across Nigeria in its quest to overthrow the government and create an Islamic state.
Boko Haram has admitted attacking several churches across the country on Christmas Day 2011, killing nearly 40 people at one church outside the capital, Abuja, alone.
It has also claimed responsibility for a string of bomb blasts around Jos on Christmas Eve 2010 that killed at least 80 people.
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