Irina Rudykh and Anton Palatkin were detained in Katmandu in August 2006 on suspicion of killing a Nepalese girl who helped Rudykh with household chores. They were convicted two years later despite a lack of evidence and alibis provided by the suspects.
"The court studied the arguments provided by the Russians' lawyers, found no grounds for the guilty verdict and revoked it on June 26," the ministry said.
The ministry said Palatkin had flown to Russia on June 30 and Rudykh planned to leave Nepal later this week.
Nepal, which is struggling to overcome the legacy of a 10-year Maoist rebellion, is notorious for arbitrary detentions and poor treatment of those in police custody. It can take years for a case to come before a judge.
The court had reportedly based the ruling on the suspicions of the victim's family.
The ministry also said the Russian nationals' visas had expired when they were arrested, and Rudykh had a fake visa. The Russians paid a total of $5,500 for violations of the visa regulations.
The Himalayan nation of Nepal is a popular tourist destination thanks to spectacular scenery and ancient Hindu and Buddhist cultures. It recently abolished its monarchy following elections that saw former Maoist insurgents win the most seats in parliament.
