Ms Taubira was known to disagree with the controversial proposals,
The citizenship plans were put forward after the 13 November Paris attacks in which 130 people were murdered.
"Sometimes staying on is resisting, sometimes resisting means leaving," she tweeted.
Ms Taubira, one of France's few senior black politicians, has been replaced by Jean-Jacques Urvoas who is seen as a supporter of the constitutional change.
Born in French Guiana, Ms Taubira has suffered racist taunts from the far-right during her time as justice minister.
A communique from the Elysee Palace said that President Francois Hollande had accepted the justice minister's decision to resign.
"They agreed on the need to bring her role to an end at a time when debate on constitutional revision begins in the National Assembly, today," the statement read.
President Hollande also praised her part in pushing through same-sex marriage laws.
Last month the justice minister made plain her distaste of the plan to strip citizens with dual nationality of their French citizenship, arguing it " would not help the fight against terrorism in any way".
However, she appeared beside Prime Minister Valls when he announced the proposals. Mr Valls has described the reform as a "strong symbolic act against those who have excluded themselves from the national community".