Goals from Vicktor Fayzulin (30) and a penalty from Roman Shirokov (78) sealed three points for the home side, who claimed the win despite never really hitting top form.
A lovely cutback from Aleksandr Kerzhakov enabled Fayzulin to slip the ball beyond the stricken visiting goalkeeper Roy Carroll, who was playing his first competitive match for his country in six years. The 34-year-old performed well in a workmanlike if uninspiring performance by his country.
Shirokov finished matters off when he sent Carroll the wrong way from the spot after Gareth McAuley was harshly deemed to have felled Russia substitute Aleksandr Kokorin as he sped into the area.
McAuley was booked, but almost netted himself on 80 minutes when his header was hacked off the line by goalscorer Fayzulin.
Northern Ireland must look to pick themselves up when they host Luxembourg on Tuesday night while Russia - group favourites alongside Portugal - face a potentially tricky test when they visit Israel.
In truth, Russia were always the more dangerous side as Northern Ireland worked hard to restrict their opponents' movements in the final third.
Carroll was forced to plunge to his right to repel a stinging Kerzhakov shot on nine minutes before doing likewise to deny the forward after he had been set up by the roving Alan Dzagoev, who was mysteriously taken off in the second half despite causing no end of problems with his movement.
McAuley was fortunate to avoid conceding a penalty on 15 minutes when he was clearly late on Vladimir Bystrov. Kerzhakov had a glorious chance to score, but ended up screwing the shot wide from inside the area.
The one-way nature of the contest continued throughout the match as Kerzahov headed over the bar on 32 minutes after Carroll had denied Shirokov with a brilliant stop.
Northern Ireland were probably relieved to reach half-time trailing 1-0 and were thankful to see Vasili Berezutski nod wide of goal from Dmitri Kombarov's corner on 54 minutes.
Kerzhakov saw a free-kick come back off a post after Bystrov had appeared to dive to win a free-kick on 77 minutes before Russia finished off the match as a contest a minute later.
Northern Ireland appealed for a penalty when McAuley smashed a volley at goal that seemed to come off the elbow of Shirokov, but it would have been harsh on the Russian player after the ball was struck with some venom.
- Aleksandr Kerzhakov
- Roman Shirokov
- Roy Carroll