The Chadians were seen piling into a convoy of several dozen cars and taxis in the capital Bangui under the taunts of angry residents looking on.
French peacekeepers kept the protesters at a distance from the convoy as the Chadians jostled to cram their personal belongings into the cars.
A first convoy of Chadian civilians left Friday, also under the jeers of angry protesters.
Military and humanitarian officials said at least one civilian was killed and several children were wounded when Chadian soldiers protecting the convoy threw grenades into the crowd.
French and African troops - including a Chadian contingent - are struggling to contain the unrest that has wracked the impoverished country since a March coup by mostly Muslim Seleka rebels who installed Michel Djotodia as interim president.
More than 1,000 people are believed to have been killed in three weeks of sectarian violence in Bangui alone.
Soldiers from mainly Muslim Chad, which lies to the north of the Central African Republic, have been accused of siding with the Seleka force, and the African Union has said the Chadians will redeploy outside the capital to avoid tensions.
The accusations have been fanned by several incidents, including one on Monday when Burundian troops in the African Union force said Chadian soldiers opened fire on them as they were disarming former rebels.
The same day, Chadian peacekeepers fired on a stone-throwing crowd of mostly Christian protesters, killing one man and wounding around 40 more.
The aftermath of the coup saw many former rebels - including some from Chad - carry out exactions against Christians, who in turn set up vigilante squads seeking revenge.