The call, made at a Cairo conference organised by Al-Azhar, came just days after Pope Francis pressed the world's Muslim leaders to condemn terrorism carried out in the name of Islam by groups such as the Islamic State (IS) and Al-Qaeda, and called for an end to the persecution of Christians in the Middle East.
"We condemn the forced exile of Christians and other religious or ethnic groups," the conference said in a final statement.
"We urge Christians to stay rooted in their homelands and to weather this wave of terrorism we all are suffering."
Accusing extremist militants of distorting the meaning of jihad, the statement said it is really one of "self-defence or repelling aggression and should not be left to a single individual or group to declare."
"All armed groups and sectarian militias who use violence and terrorism... have no relationship with true Islam," it said.
IS has seized swathes of territory in Iraq and Syria, carrying out mass executions, kidnappings, rapes and beheadings.
It has also tyrannised Christians by forcing them to choose between conversion to Islam or paying protection money, telling them otherwise they must flee on the pain of death.
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The Cairo conference offered no firm plan to curb jihadists, but it called for another international forum to be convened to "spread justice and respect for different beliefs."
On Sunday, Pope Francis said he had told President Recep Tayyip Erdogan during a visit to Turkey that "it would be wonderful if all the Muslim leaders of the world -- political, religious and academic -- spoke up clearly and condemned" violence that damages Islam.
"That would help the majority of Muslims if that came from the mouths of these political, religious and academic leaders. We all have need of a global condemnation."
In remarks Wednesday, Al-Azhar head Sheikh Ahmed al-Tayeb directly condemned IS for its "barbaric crimes" and urged the US-led coalition fighting it to crack down on countries which support terrorism financially and militarily.
The United States launched its first air strikes against IS in Iraq in August. In late September, it extended the campaign to IS targets in Syria, joined by Arab allies.
Islamic scholars from a number of Muslim countries, including Saudi Arabia, Iran, Malaysia, Indonesia and Morocco, attended the Cairo conference.