"I thank the president who gave me this liberation," Ingabire said as she left Mageragere Prison in the capital Kigali.
"This is the beginning of the opening of political space in Rwanda, I hope so," she said calling on Kagame "to release other political prisoners".
The surprise release of 2,140 prisoners, including Ingabire and musician Kizito Mihigo, followed a cabinet meeting on Friday at which a presidential order of "mercy" was approved.
"The Cabinet meeting chaired by President Paul Kagame today approved the early release of 2,140 convicts found eligible under relevant provisions of law," a justice minister statement read.
"Among them are Mr Kizito Mihigo and Ms Victoire Ingabire Umuhoza, the remainder of whose sentences were commuted by Presidential prerogative following their most recent applications for clemency in June this year."
Ingabire returned from exile in The Netherlands intending to run for president in 2010 as leader of the FDU-Inkingi party.
However, she was arrested, charged with terrorism and treason and sentenced to 10 years in jail during a widely criticised trial.
Ingabire, an ethnic Hutu, was accused of "genocide ideology" and "divisionism" after publicly questioning the government narrative of the 1994 genocide of mostly Tutsi people that killed around 800,000 people.
On appeal, Rwanda's Supreme Court extended her sentence to 15 years.
Stability and repression
In November last year, the Arusha-based African Court on Human and Peoples' Rights ruled that Rwanda had violated Ingabire's rights to freedom of speech and adequate defence, prompting calls for a retrial.
However, Rwanda ignored the ruling.
Members of Ingabire's party -- which has not been permitted to register -- have frequently been arrested during her detention, and human rights groups have accused the military of torturing them.
Rwandan musician Kizito Mihigo was arrested in 2015 and jailed for 10 years for conspiring to assassinate Kagame.
Kagame, the country's de facto ruler since his rebel army stopped the genocide in 1994, recently changed the constitution clearing the way for him to rule until 2034.
Another opposition politician, Diane Rwigara, who sought to challenge for the presidency in 2017, was blocked by the electoral commission and subsequently arrested and charged with treason. Her trial is underway.
Others presidential challengers have been prevented from entering the country, while exiled dissidents have been threatened and sometimes murdered.
Kagame has been praised for bringing stability and economic growth to his tiny nation but often comes under fire for restricting political freedom.
He commonly wins re-election with over 90 percent of the vote.
Although Rwanda is constitutionally a multi-party system there is practically no opposition within the country with most of the recognised parties supporting the ruling Rwandan Patriotic Front (RPF).
However, in parliamentary elections earlier this month the opposition Green Party won two seats, for the first time.
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