The announcement by Chadian Communication Minister Hassan Sylla Bakari came after days of talks between Djotodia's supporters and rival groups, the Wall Street Journal reported.
Djotodia and his prime minister, Nicolas Tiengaye, who also resigned, participated in some of the talks, Bakari said.
Djotodia came to power in March 2013 during an armed rebellion.
Opposition leader Martin Ziguele, a former prime minister, said Djotodia's resignation "will now lead the country to peace and reconciliation. But it will need the full and honest collaboration of all Central Africans to join hands in this effort to achieve lasting peace."
In a statement presented to members of the summit, U.N. Secretary-General Ban Ki-moon urged an immediate end to "the horrific cycle of violence and retaliation" between groups in the Central African Republic.
Warning of a real danger of more conflict along religious lines, Ban said, "distrust is high and violence has fueled anger and a thirst for revenge."
He said leaders at the summit should plan for new election in CAR, as well the demobilization and reintegration of the former fighters.
The conflict has left thousands dead. Nearly a quarter of the country's population, about 1 million people, have been driven from their homes, while about 2.2 million people are in need of humanitarian assistance.