The airline was avoiding flying over Belarus due to the recent plane diversion and arrest of a journalist.
The biofuel used for Tuesday's flight was "made from waste and residue sourced from the circular economy," according to Air France-KLM.
Air France has expressed its "deepest sympathy and compassion for this human tragedy."
Singapore Airlines changed route to avoid the northern part of the Sea of Japan.
A petition calling on the airline to let gay stewards opt out of the Tehran route has been signed by 23,000 people.
The attacks in Paris resulted in 130 deaths in November.
The November 13 attacks in Paris killed 130 people and injured hundreds.
The airline had suspended direct flights between Paris and Tehran in 2008 for economic reasons.
U.S. and Canadian officials have searched both planes and determined them safe
Bosses had shirts torn from their backs after 3,000 job cuts were announced.
U.S. fighter jets escorted the plane to JFK on Monday after an anonymous caller made a bomb threat involving commercial aviation.