Jamatul Ahrar, an offshoot of the Tehreek-e-Taliban, claimed responsibility for the deadly attack, news web sites said.
At least 78 people were hurt in the explosions at the Catholic Church and Christ Church in the city’s Youhanabad area, home to the country’s biggest Christian population.
The condition of 30 of the injured was stated to be critical, media reports said.
A large crowd was already in the area to attend the Sunday prayers and violent protests erupted in the area immediately following the blasts.
Television footage showed dozens of stick-wielding men, mostly belonging to the Christian community, ransacking the metro bus terminal in the city, Dawn online reported.
Enraged protestors held four injured policemen captive at a shop after the blast for allegedly watching a cricket match instead of performing their duties at the time of the bomb attack.
Witnesses said suicide bombers were responsible for the explosions but police have not confirmed this, a BBC report said, adding that the bombers are said to have detonated their explosives at the gates of the churches.
According to the report in Dawn online, Rana Mashood, a government spokesperson, said the government was determined to tackle the issue of militancy and added that “terrorists will be brought to justice”.
He said they were not looking at the event as an attack on a particular community or members of one religion.
“We are not separated by religion, this is an attack on Pakistan, and we feel their pain,” the media report quoted Punjab education minister Mian Mujtuba Shuja-ur-Rehman as saying.
Sunday’s attack is the worst on the community since 2013, when twin suicide attacks at the All Saint’s Church in Peshawar’s Kohati Gate area killed 80 people and wounded over 100 others.
Meanwhile, missionary schools in Karachi and across Punjab will remain closed on Monday in protest against the attack.
President Mamnoon Hussain and Prime Minister Nawaz Sharif have strongly condemned the blasts.