Father Peter Umoren, a parish priest, told journalists he had begun Mass when an explosion rocked the church.
"I was right on the pulpit when we heard the heavy explosion," Father Umoren said.
"The church building almost collapsed on the congregation, but God saved us, that the roof did not come down but the ceilings were shattered," he said.
That evening, gunmen killed three Christians in a village south of the city, said Pam Ayuba, Plateau state spokeswoman. She said officials did not believe the shootings were connected to the earlier church violence.
The incidents are the most recent in a decade-long conflict among Christians and Muslims that has claimed thousands of lives in and around Jos.
Ayuba said the blast damaged the church's roof, blew out its windows and destroyed a portion of the fence surrounding the church's compound, the Associated Press reported.
The bombing led to retaliatory violence by youths who set fire to homes. Soldiers guarding the city opened fire in neighborhoods, witnesses said.
Government and relief officials told Agence France-Presse that in addition to those killed in the bombing and afterward, 24 people were injured, including several soldiers. Several of the victims were critically injured, authorities said.
No group immediately claimed responsibility for the bombing. Various sites in Jos have been targeted by Boko Haram, which the Nigerian government considers an extremist Islamist sect. The loosely connected organization has claimed credit for a series of bombings on Christmas Eve 2010 that killed as many as 80 people and a similar church bombing Feb. 26 on the headquarters of the Church of Christ that left three dead and 38 wounded.
Nigerian President Goodluck Jonathan condemned the bombing and reaffirmed the government's determination "to end the space of mindless attacks and killings."
Jos remained tense March 12 as businesses and shops reopened. People said they feared a repeat of deadly riots that followed the Feb. 26 attack.