Ikechukwu Uche's penalty and Aaron Samuel's strike provided the perfect tonic to Nigeria's recent woes, with Stephen Keshi back in the dugout even as uncertainty continues to surround his future.
A tight first half yielded few clear-cut chances, but the visitors made the breakthrough just before the hour mark when Emmanuel Emenike was brought down inside the box and Uche kept his cool from the spot.
Thievy Bifouma missed a penalty for the hosts five minutes later and Samuel wrapped up the points with a tidy finish from Samuel in the last minute, with angry home fans causing a slight delay when they threw missiles onto the pitch.
The result moves Nigeria into second place, with goal difference pushing them ahead of Congo heading into the final round of games in Group A.
Congo started brightly and saw Bifouma spurn two presentable chances inside the opening 10 minutes, while Fode Dore also skewed wide when well placed seven minutes before half-time.
The visitors suffered an early blow after the interval when Hope Akpan went off injured, but they broke the deadlock soon after.
Chancel Massa fouled Emenike in the box and Uche beat the goalkeeper with a low finish into the bottom-left corner from 12 yards.
Congo were given a chance to level the scores with a penalty of their own after Godfrey Oboabona was adjudged to have handled a Prince Oniangue shot.
Bifouma stepped up to take the kick, but Vincent Enyeama guessed correctly and pushed the striker's effort away to ensure Nigeria's lead remained intact.
After Uche had wasted two chances to double Nigeria's lead, the hosts saw efforts from Francis N'Ganga and Delvin Ndinga go close, the latter denied by a great save from Enyeama
A swift counter-attack following that save saw Nigeria secure their victory, substitute Samuel curling a left-footed effort beyond Massa to give Keshi a winning return.
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