At least four French armoured vehicles took up positions near the presidential palace in Bangui after Djotodia's resignation was announced.
Djotodia's presidential guards are stationed nearby and have a number of heavy weapons.
After a meeting with the CAR's entire provisional parliament until 4.00am, the Economic Community of Central African States (Eccas) announced the resignations at the end of its meeting on Friday.
The summit on Thursday suspended its debate on the crisis-hit coutry in order to fly all 135 members of the National Transitional Council from Bangui to N'Djamena.
With Chadian President Idriss Déby, the current Eccas head, leading the charge, they told them that the two, whose mutual relationship is notoriously bad, had to go.
The CAR's "own sons" had plunged the pay into a "war that dangerously compromises its future", Déby told the summit, putting the blame on "the political class in its entirety".
In Bangui thousands of people demonstrated near the airport on Friday to oppose Djotodia's return.
After weeks of sectarian violence, Bangui has been relatively calm this week, however.
"The situation is improving - slowly, but it is improving," the commander of the French troops in the CAR, General Francisco Soriano, said on Thursday.