Two years ago, he was sentenced to 25 years for terrorism by a Rwandan court in what supporters called a sham trial.
A government spokesperson said Mr Rusesabagina's sentence had been "commuted by presidential order".
Mr Rusesabagina, 68, is credited with saving some 1,200 people during the 1994 genocide.
US President Joe Biden called the news of his release a "happy outcome".
"Paul's family is eager to welcome him back to the United States, and I share their joy at today's good news," he said in a statement.
It has taken years of diplomatic pressure and talks brokered by Qatar for Mr Rusesabagina to be released.
Much of that pressure came from the United States, where he had lived since 2009. The Biden administration has said he was "wrongfully detained".
Mr Rusesabagina's family say the Rwandan government lured him from Texas, where he had permanent residency, back to Rwanda in 2020.
He left Rwanda in 1996. His story remained largely unknown for a decade, while he worked as a taxi driver in the Belgian capital, Brussels.
It was featured in a section of journalist Philip Gourevitch's 1998 book about the genocide, but it was the 2004 Hollywood movie, where he was played by Don Cheadle, that brought him global attention.The Rwandan genocide lasted 100 days from April 1994, when 800,000 people, mostly from the Tutsi ethnic group, were slaughtered by extremists from the Hutu community.
Mr Rusesabagina - a hotel manager at the time - protected some 1,200 people from the violence, after they sought shelter in the building.
The following year he was awarded the Presidential Medal of Freedom by then-US President George W Bush for his efforts. But he became a fierce critic of Rwanda's President Paul Kagame.
In a 2018 video message, Mr Rusesabagina called for a regime change, saying that "the time has come for us to use any means possible to bring about change in Rwanda".
He was arrested in 2020, when, according to his supporters, a private jet he believed would take him to Burundi, instead landed in the Rwandan capital Kigali.
In September 2021 he was found guilty of backing a rebel group behind deadly attacks in 2018 and 2019 in Rwanda.
Mr Rusesabagina was freed alongside Callixte Nsabimana, spokesman of the Rwanda Movement for Democratic Change - an opposition political party.
A spokesperson for the Rwandan government said: "No-one should be under any illusion about what this means, as there is consensus that serious crimes were committed, for which they were convicted.
"Under Rwandan law, commutation of sentence does not extinguish the underlying conviction.
"Rwanda notes the constructive role of the US government in creating conditions for dialogue on this issue, as well as the facilitation provided by the state of Qatar."