Toussaint's interval of freedom from foreign confrontation was unfortunately brief. Toussaint never severed the formal bond with France, but his de facto independence and autonomy rankled the leaders of the mother country and concerned the governments of slave-holding nations, such as Britain and the United States. French first consul Napoléon Bonaparte resented the temerity of the former slaves who planned to govern a nation on their own. Moreover, Bonaparte regarded Saint-Domingue as essential to potential French exploitation of the Louisiana Territory. Taking advantage of a temporary halt in the wars in Europe, Bonaparte dispatched to Saint-Domingue forces led by his brother-in-law, General Charles Victor Emmanuel Leclerc. These forces, numbering between 16,000 and 20,000--about the same size as Toussaint's army--landed at several points on the north coast in January 1802. With the help of white colonists and mulatto forces commanded by Pétion and others, the French outmatched, outmaneuvered, and wore down the black army. Two of Toussaint's chief lieutenants, Dessalines and Christophe, recognized their untenable situation, held separate parleys with the invaders, and agreed to transfer their allegiance. Recognizing his weak position, Toussaint surrendered to Leclerc on May 5, 1802. The French assured Toussaint that he would be allowed to retire quietly, but a month later, they seized him and transported him to France, where he died of neglect in the frigid dungeon of Fort de Joux in the Jura Mountains on April 7, 1803.

The betrayal of Toussaint and Bonaparte's restoration of slavery in Martinique undermined the collaboration of leaders such as Dessalines, Christophe, and Pétion. Convinced that the same fate lay in store for Saint-Domingue, these commanders and others once again battled Leclerc and his disease-riddled army. Leclerc himself died of yellow fever in November 1802, about two months after he had requested reinforcements to quash the renewed resistance. Leclerc's replacement, General Donatien Rochambeau, waged a bloody campaign against the insurgents, but events beyond the shores of Saint-Domingue doomed the campaign to failure.

By 1803 war had resumed between France and Britain, and Bonaparte once again concentrated his energies on the struggle in Europe. In April of that year, Bonaparte signed a treaty that allowed the purchase of Louisiana by the United States and ended French ambitions in the Western Hemisphere. Rochambeau's reinforcements and supplies never arrived in sufficient numbers. The general fled to Jamaica in November 1803, where he surrendered to British authorities rather than face the retribution of the rebel leadership. The era of French colonial rule in Haiti had ended.

On January 1, 1804, Haiti proclaimed its independence. Through this action, it became the second independent state in the Western Hemisphere and the first free black republic in the world. Haiti's uniqueness attracted much attention and symbolized the aspirations of enslaved and exploited peoples around the globe. Nonetheless, Haitians made no overt effort to inspire, to support, or to aid slave rebellions similar to their own because they feared that the great powers would take renewed action against them. For the sake of national survival, nonintervention became a Haitian credo.