Rusesabagina was released late Friday away from the media glare and will return to the United States after the Kigali government commuted his 25-year sentence on terrorism charges.
His detention had thrown a spotlight on Rwanda's record of crushing political dissent and free speech under President Paul Kagame.
Rusesabagina was convicted in September 2021 of backing an armed rebel group after a trial that his supporters denounced as a sham.
The 68-year-old, who is also a Belgian citizen with U.S. permanent residency, has been in failing health and his family said he was tortured during his 939 days in detention.
Shortly before midnight Friday, Rusesabagina arrived at the Qatari ambassador's residence in Kigali, a U.S. official said.
He will likely stay there for "a couple of days" before flying to Qatar, which helped broker his release, and then to the United States, another US official said.
His sentence was commuted by presidential order, Justice Minister Emmanuel Ugirashebuja said in a statement, while 19 co-defendants also saw their sentences commuted.
But the minister warned: "Under Rwandan law, commutation of sentence does not extinguish the underlying conviction."
U.S. President Joe Biden welcomed Rusesabagina's release, calling it 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.
U.S. Secretary of State Antony Blinken said in a statement Friday that the United States was "grateful" to Rwanda for the release, while Belgium also said it welcomed the move.
Rwanda praised the role of both the United States and Qatar in resolving the case.
"This is the result of a shared desire to reset (the) US-Rwanda relationship," Kagame's press secretary Stephanie Nyombayire tweeted Friday, adding the close relationship between Rwanda and Qatar was "key."
Talks on a potential release started at the end of 2022 and a breakthrough came last week in discussions between Kagame and Qatar's emir, Sheikh Tamim bin Hamad al-Thani, a source with knowledge of the negotiations said.
