Michael Paterson's 43rd-minute header sent the home crowd into raptures and was enough to give Michael O'Neill his first win as Northern Ireland boss.
O'Neill's men more than held their own in Belfast and could have been in front when Jamie Ward's ferocious strike cannoned back off the post in the first half.
But only minutes later, Naill McGinn's pinpoint cross was expertly headed in by Paterson to end a 12-game winless streak.
Russia boss Fabio Capello had caused controversy in the run-up to the match, stating "it's only Northern Ireland", but the Italian coach will be regretting those comments after this surprise result.
The men in green worked tirelessly right from the word go, harrying their opponents into mistake after mistake.
And the home side had several half chances of their own early on, with McGinn and Shane Ferguson causing problems down the flanks.
But just after Ward had seen his effort come back off the woodwork, McGinn did well to reach a long ball and delivered the ball in the area, where Paterson rose above the Russian rearguard to give his side a shock lead at the break.
The Eastern Europeans made a few changes for the second-half, with Artyom Dzyuba injecting some urgency into their attacks.
However, with Gareth McAuley and Craig Cathcart imperious at the back, the visitors never really troubled home goalkeeper Roy Carroll.
In fact, the home side could have extended their advantage, with Paterson having the ball in the net again, but he was adjudged to have been in an offside position.
The final whistle was greeted with scenes Windsor Park hasn't seen for a long time, and after just two wins in their past 33 games, it was certainly long overdue and keeps alive their faint qualification hopes.