In a message to German Chancellor Angela Merkel late on Tuesday, President Rouhani expressed his "great sorrow" over the tragic incident and extended condolences on behalf of the Iranian nation and government to the people and government of Germany and the victims' families.
Iranian Foreign Ministry Spokeswoman Marziyeh Afkham also offered her condolences to the bereaved families of those killed in the jet crash.
A German A320 Airbus ploughed into an Alpine mountainside on Tuesday, killing all 150 people on board including 16 schoolchildren returning from an exchange trip to Spain.
The A320 jet operated by Lufthansa's Germanwings budget airline was obliterated when it went down in a rugged area of ravines while flying over southern France en route to Duesseldorf from Barcelona.
No distress call was received from the aircraft, but France said one of the two "black box" flight recorders had been recovered from the site 2,000 meters (6,000 feet) above sea level.
Lufthansa said it was working on the assumption that the tragedy had been an accident, adding that any other theory would be speculation.