"The leaders expressed the absolute necessity for tolerance and peace in all our communities, and that incitement to violence, hate and intolerance, due to our different ideological and religious viewpoints, [is] unacceptable in Islam," said MJC secretary general Shaykh Isgaak Taliep.
The majority of Muslims in South Africa are Sunni but there is a growing Shia community.
MJC president Shaykh Irafaan Abrahams, and his deputy, Maulana Abdul Khaliq Ebrahim Allie, led the delegation and condemned the attack "in the strongest possible terms".
The Hawks are investigating the attack.
On Thursday, Abbas Essop was stabbed to death, and Imam Ali Nchiyane, was stabbed three times, but survived.
The attackers also burnt the Quran and Islamic literature when the mosque was set alight after the stabbing.
Caretaker Mohamed Ali was also injured in the attack, which was followed by the discovery of a bomb in the mosque a few days later.
The incident happened days before Muslims worldwide begin fasting during the holy month of Ramadan.
The mosque is aligned with the Shia branch of Islam and the Cape Town community has already indicated that it is planning to bring in extra security for its recently-opened center in Ottery.
In its statement, the MJC said: "It is common fact that historic differences between Shia and Sunni do exist within the community, and in a very matured and conciliatory discussion, the leaders acknowledged that this should not lead to hatred and violence used by elements who seek to divide our communities along sectarian lines."
The MJC delegation also visited Essop's family to express condolences after the "productive" meeting at the mosque.
The ANC caucus in the Johannesburg council also condemned the attack on the mosque, in a joint statement with its alliance partner in council, the Al Jama-ah party.
"We strongly condemn the burning of the mosque and the killings, which recently took place in KwaZulu-Natal," Al Jama-ah councillor Thapelo Amad said.