In a telegram sent to French President Francois Hollande, published by the Kremlin, Putin said he was "shocked by the news" after De Margerie's jet crashed into a snow plough at Moscow's Vnukovo airport, killing all on board.
Putin asked Hollande to "pass on the most sincere condolences and words of sympathy" to De Margerie's family and loved ones.
He praised the 63-year-old oil boss as "an outstanding French entrepreneur who originated many major joint projects that formed the basis of many years of fruitful cooperation between Russia and France in the energy sector."
Putin's spokesman Dmitry Peskov earlier told Russian news agencies that the president had known the French oil boss for a long time and "highly esteemed De Margerie's business qualities and his consistent devotion to developing not only bilateral Russia-French relations, but also mutually rewarding multi-faceted cooperation as a whole.