The Airbus 320 took off at 1.30am Moscow time from the Russian capital's Domodedovo airport.
Regular commercial flights between the two countries were cut in 2004 when a US-led coalition overthrew Saddam Hussein's regime.
Russian and Iraqi authorities have been in negotiations to restart flights since 2015.
Moscow and Baghdad recently strengthened military ties with Iraq purchasing Russian T-90 battle tanks this month.
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