Mr Djotodia resigned his post on Friday, at a summit aimed at ending the ongoing sectarian violence.
He was met off the plane by Benin's foreign minister, Nassirou Bako Arifari.
At least 1,000 people have been killed since violence broke out between Christians and Muslims in December.
Mr Djotodia's resignation, and that of his Prime Minister Nicolas Tiengaye, appear to have failed to quell the
violence in the CAR's capital, Bangui.
Clashes between rival militias have continued since his departure. The Red Cross said at least six people were killed in Bangui.
Muslim homes and shops have reportedly been looted.
The resignation of President Djotodia sparked jubilation among Christians in the strife-torn capital Bangui The French news agency AFP reports sporadic gunfire, with several people killed, and quotes some residents as
saying they saw shocking incidents of cannibalism.
Spiralling into violence Michel Djotodia, CAR's first Muslim leader, seized power last year.
But although he officially disbanded the Seleka rebels who enabled him to take the presidency, he has proved unable to keep them in check.
Their actions prompted Christians to form vigilante groups, sparking a deadly cycle of revenge attacks.
Since he seized power, 20% of the population have fled fighting between Christian and Muslim militias.
The African Union now has some 4,000 peacekeepers in the country and France has deployed 1,600 troops to try to restore peace.
Following Mr Djotodia's resignation announcement, thousands of people took to the streets in Bangui, most of
them Christians who were celebrating the news.
Muslims largely stayed at home, the BBC's Paul Wood reports from Bangui.
Many Christians now want to go back to the way things were with their Muslim neighbours, our correspondent says.
Meanwhile, the International Organisation for Migration has begun airlifting thousands of foreigners out of the country.
The first flight evacuated some 800 Chadians, according to AFP.
The UN has warned of an impending humanitarian disaster in the country.
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