Some 129 members of the National Transitional Council (CNT), which serves as an acting parliament with 135 members in all, were taking part in the vote aimed at replacing Michel Djotodia, who was forced to stand down on January 10.
"It won't be easy" for the new leader, Kouyassoum Doumta said, urging her colleagues to "spare a thought" for "abandoned" civilians in the provinces and for hundreds of thousands of displaced people.
Each presidential candidate was given 10 minutes to make a "statement of intent" to the CNT members, who were then set to choose a new transitional leader by secret ballot in a single round.
The parliamentary body decided that in order to be elected, a candidate must win the absolute majority in that round. Failing this, a second round will pit the two front-runners against each other.
Some Christian communities responded by forming "anti-balaka" (anti-machete) self-defence militias and attacking Muslims. Both sides are accused by rights watchdogs of major abuses and the United Nations has warned of a potential inter-religious "genocide".
