The Northern Irish started the brighter of the two sides, but there was little in the way of real goalmouth activity until Jamie Ward finished off a long run with a well-struck effort that hit the base of Russian stopper Igor Akinfeev's left-hand post after 40 mins.
Two minutes later, O'Neill's side had the lead when Paterson rose highest from an inviting cross from Niall McGinn to head beyond Akinfeev and send the home side in 1-0 up at the break.
Paterson then had a second disallowed on the hour mark when he turned the ball home, only to see the offside flag go up.
Sensing victory was within their grasp, the Northern Irish settled their play and composed themselves and restricted their opponents to speculative efforts from long range.
Victory takes Northern Ireland up to fourth with six points in Group F, while the Russians stay second on 12 points from five games.