The Azerbaijan Airlines jet then crash-landed near Aktau in Kazakhstan, killing 38 of the 67 on board.
Most of the passengers on the flight were from Azerbaijan, with others from Russia, Kazakhstan and Kyrgyzstan.
It is believed most of those who survived were seated in the plane’s rear.
Flight J2-8243 had been en route from the Azerbaijan capital of Baku to the Chechen capital of Grozny on 25 December when it came under fire and was forced to divert.
The Kremlin released a statement on Saturday noting Putin had spoken to Azerbaijan’s president Ilham Aliyev by phone.
“(President) Vladimir Putin apologised for the tragic incident that occurred in Russian airspace and once again expressed his deep and sincere condolences to the families of the victims and wished a speedy recovery to the injured,” it said.
In the rare publicised apology, Putin also acknowledged the plane had repeatedly tried to land at Grozny airport in Chechnya.
At the time, the cities of Grozny, Mozdok and Vladikavkaz were “being attacked by Ukrainian unmanned aerial vehicles, and Russian air defence systems repelled these attacks”, he said.
The Kremlin read-out made no direct admission that the plane had been struck by Russian missiles.
In a statement released a shortly after the Kremlin’s, Ukrainian President Zelensky said the damage to the aircraft’s fuselage was “very reminiscent of an air defence missile strike”, adding that Russia “must provide clear explanations”.
“The key priority now is a thorough investigation that will answer all questions about what really happened.”
Prior to Saturday, the Kremlin had refused to say whether it was involved in the crash with authorities saying they were awaiting investigation results.
But Russian aviation authorities had earlier in the week said the situation in the region was “very complicated” due to Ukrainian drone strikes.