Jacqueline Sauvage, 68, had become a symbol of the scourge of domestic violence in France and a cause célèbre, with almost 400,000 people signing a petition calling on François Hollande to use his rarely used presidential right of pardon.
Ms Sauvage was married for 47 years to Norbert Marot, a violent alcoholic whom she said raped and beat her and her three daughters and also abused her son.
On September 10, 2012, the day after her son hanged himself, Ms Sauvage shot her husband three times in the back with a rifle.
She was found guilty of murder and sentenced to 10 years in prison in October 2014, which was upheld on appeal in December 2015 as the state rejected her pleas of self-defence.
The Socialist leader agreed to meet her three daughters and lawyers on Friday, and afterwards said he needed "time to think" before making the decision about the pardon.
On Sunday evening, his office said he had granted the pardon and that Ms Sauvage could immediately request her release.
“The president of the republic, faced with this exceptional human situation, wants to enable the return as soon as possible of Ms Sauvage to her family,” it said in a statement.
During his 2012 presidential campaign, Mr Hollande distanced himself from such pardons, reinstated by Napoleon, describing them as belonging to "a different concept of power".
He has granted only one to date, when he freed convicted bank robber Philippe El Shennawy – who had spent 38 years behind bars – in 2014.
When Ms Sauvage was sentenced, the activist group Osez le Feminisme (Dare To Be Feminist) called for the definition of self-defence to be expanded in cases of "female victims of violence".
Even Fleur Pellerin, Mr Hollande's culture minister, said she was "overwhelmed" by the testimonies of the daughters and said: "We are in the presence of an exceptional case."