In a message to Malaysian Prime Minister Najib Razak, Rouhani expressed deep sorrow and grief over the incident and offered heartfelt condolences to the Malaysian premier and nation.
The president also prayed for patience for the bereaved families in coping with this tragic event.
He further said such incidents and the ensuing grief of nations more than before highlights the need for the world community to return to peaceful coexistence and avoid violence and conflict.
Malaysia Airlines plane flight MH17 was shot down over eastern Ukraine on Thursday.
Both the government and the pro-Russia separatists fighting in the region denied any responsibility for downing the aircraft.
Plumes of black smoke rose up near a rebel-held village of Hrabove, 40 kilometres from the Russian border.
The Boeing 777-200ER plane, travelling from Amsterdam to Kuala Lumpur, appeared to have broken up before impact and the burning wreckage - which included body parts and the belongings of passengers - was scattered over a wide area.
Malaysia Airlines said Ukrainian aviation authorities told the company they had lost contact with MH17 at 1415 GMT (2.15am NZT).
It said the plane was carrying 280 passengers and 15 crew.