The 68-year-old former hotelier landed in Doha on Monday, Rwanda's government spokesperson Yolande Makolo told Reuters..
From Doha, he will return to the United States, U.S. officials have said.
Rusesabagina, a U.S. permanent resident, was sentenced in September 2021 to 25 years over his ties to a group opposed to Rwandan President Paul Kagame that has an armed wing.
He was released on Friday after his sentence was commuted following months of negotiations between Washington and Kigali.
Rwanda has said that Rusesabagina's release is the result of a shared desire to reset the U.S.-Rwanda relationship.
"Hotel Rwanda" portrays Rusesabagina's success in saving more than 1,000 people during the genocide in 1994 by sheltering them in the besieged hotel that he managed in Kigali.
During his trial Rusesabagina acknowledged having a leadership role in an opposition group but denied responsibility for attacks carried out in Rwanda by its armed wing.
The trial judges said the two wings of the group were indistinguishable.
In a letter to Kagame earlier this month, Rusesabagina wrote that if he was pardoned and freed, he would abandon politics and spend the rest of his days in the United States "in quiet reflection."
Washington's historically close ties with Rwanda have been strained by Rusesabagina's detention and by U.S. allegations, denied by Kigali, that Rwanda has sent troops into neighboring Democratic Republic of Congo and supports rebels there.