Mr Djotodia, who proclaimed himself head of state after the Seleka rebels took control of the capital, Bangui, was the only candidate in the vote.
Former President Francois Bozize fled overseas as the rebels advanced.
Mr Djotodia has said he will hold elections within 18 months.
He originally said there would be a three-year wait before polls.
The Seleka rebels, an alliance of armed groups, seized power after a peace deal negotiated with Mr Bozize collapsed.
Mr Djotodia is a former civil servant who fell out with Mr Bozize and went into exile, before returning under the peace deal in January as defence minister.
He resigned in March before seizing power.
Correspondents say he does not have widespread international support and has fallen out with some of his former allies.
CAR has an unstable history and is extremely poor, though it has large deposits of minerals including gold and diamonds.
The national transitional council in the Central African Republic has elected the rebel leader who seized power last month, Michel Djotodia, as interim president.