The Diocese of Nizhny Novgorod had owed a construction company the cash for a new heating system but was unable to pay the full amount back.
After only paying half of the sum the company took legal action against the Church.
Before the case got the court the owners of the business, who are devout Christians, agreed to waive the debt if the Church promised to pray for the men.
St Petersburg legal portal said it was the first time such a deal had been struck.
In a statement on the Gazeta.ru website the diocese said: "We ourselves were surprised... They even drew up the wording themselves."
The company's manager, Andrei Lepustin told the website: "We all respect the diocese and we are all Orthodox believers, it'll be on their conscience if they don't, but we trust them and have already felt the fruits of their prayers, as prosperity indicators for both the company and its employees are growing."