Hundreds of supporters surrounded his car as he left Lima's Barbadillo prison.
The nation's constitutional court reinstated a presidential pardon issued six years go to the 85-year-old.
He is a highly divisive figure having been jailed for corruption and human rights violations while in office.
The former president had been serving out a 25-year prison sentence at the time of his pardon.
Mr Fujimori left the compound wearing a face mask, supported by two of his children, Kenji and Keiko Fujimori, who lost the last presidential election by a narrow margin.
To his supporters, Alberto Fujimori was the president who saved Peru from the twin evils of terrorism and economic collapse. To his opponents, he was an authoritarian strongman who rode roughshod over the country's democratic institutions in order to preserve his hold on power.
The son of Japanese immigrants, Mr Fujimori's decade in power from 1990 to 2000 in which he ruled with an iron fist was marked by a series of dramatic twists and turns.
His authoritarian government's crackdown on two violent insurgencies during his tenure resulted in the deaths of an estimated 69,000 people.
Several years after his presidency ended, Mr Fujimori was found guilty of bribery and abuse of power and was sentenced to 25 years in prison for human rights abuses during his time in office - including authorising a number of killings carried out by death squads.
When he was sentenced to prison in 2009 at the age of 70, most Peruvians assumed the former leader would spend the rest of his life in jail.
But in December 2017, he was taken from prison to hospital because of health concerns. He was suffering from low blood pressure and abnormal heart rhythm.
That same month, Mr Fujimori was granted a pardon by President Pedro Pablo Kuczynski after doctors said his illness was incurable, adding that prison represented a "grave risk to his life".
By Leonardo Rocha & Nadeem Shad