The resignations of Mr Djotodia and his Prime Minister Nicolas Tiangaye were announced in a statement issued at a two-day summit of the Economic Community of Central African States (CEEAC) in neighbouring Chad. Talks to decide on new leadership will take place in Central African Republic, it said.
Thousands of people have been killed, and one million displaced, by cycles of violence since abuses by Mr Djotodia's mainly Muslim rebels, known as Seleka, prompted the creation of Christian self-defence militia after he seized power in March.
With memories of Rwanda's 1994 genocide stirred by the unrest, France sent hundreds of troops to its former colony last month to support African peacekeepers trying to keep the peace. But the killings have continued, and France repeatedly voiced its frustration with Mr Djotodia's government.
Mr Djotodia and Mr Tiangaye resigned after Central African Republic's transitional assembly (CNT) was summoned to the Chad summit late on Thursday to decide on the country's future.
Under an agreement brokered by the CEEAC last year, the CNT elected Mr Djotodia to his position as interim president in April to take Central African Republic to elections, due at the end of this year.
French Foreign Ministry Romain Nadal spokesman said: "We take note of the resignation.
"It is up to the CNT to decide what happens now."