The Boeing 737, which was flying from Dubai to Rostov-on-Don, exploded into a fireball after missing the runway on a second landing attempt in heavy wind and rain.
Europe's worst air crashes in past 10 years
"The airport is now fully functional," an airport representative told AFP.
Regional authorities said Sunday that workers had finished clearing the runway of debris, which investigators said had been scattered up to 1.5 kilometres (one mile) from the crash site.
Outbound flights resumed at around 0630 GMT on Monday, but incoming flights to the city of one million were still either cancelled or delayed.
Investigators have launched a criminal probe into whether poor weather, a pilot error or a technical fault were behind the crash, which killed all 55 passengers and seven crew members on board.
Air tragedy: 62 perish as Dubai plane goes down in Russia
The plane's two black boxes were recovered from the crash site but were "badly damaged", Russia's intergovernmental aviation committee said, warning that their analysis would take time.
Experts from the state-owned budget airline flydubai, a sister firm of Emirates Airlines, and the United Arab Emirates authorities are assisting with the probe, Russian investigators said.
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