In the comments to a similar but opposite question (‘Can I enter Russia 1–1.5 hours before the visa validity period starts?’), David Richerby noted:
1-1.5 hours before the visa validity starts is a time at which the visa is not valid. If you rephase "1-1.5 hours before the visa validity starts" with "without having a valid visa", your question becomes "Is it possible to enter Russia by train without having a valid visa?" The answer now seems pretty obvious.
And the opposite is true here: You are arriving two hours after your visa validity starts. You can rephrase that as ‘Can I enter Russia with a valid visa?’, to which the answer obviously is ‘yes’.
From the point of view of the Russian immigration officer handling you once you enter Russia, he doesn’t know which plane you just came from. While unfortunately there is no actual flight as far as I could tell, you may just have taken a much shorter flight, e.g. from Lithuania or the East of Ukraine which left at midnight. Or maybe you flew in from Singapore, arrive sometime in the afternoon but actually left the night before. The immigration officer won’t care; he will check the date your visa becomes valid, check if that is today or earlier and then continue to stamp you in.
Of course, the airline knows this, too. The people at the check-in desk should be aware of this; although they may slip up for a second. Politely point out that you won’t be landing until after midnight and everything should be resolved. Their job is to make sure you have a valid visa at the time you arrive not at the time you leave (which, additionally, is a time zone away from Moscow).