Villain-cum-hero Junior Ajayi scored both goals for the Nigerians early in the second half before a capacity 40,000 crowd in south-east city Port Harcourt. But Moise Nkounkou snatched a potentially crucial away goal on 66 minutes to leave the third-round tie on a knife-edge.
Celebrated France-born Congo coach Claude Le Roy is hoping to take a team to the Olympics for the first time after a success-filled career with various African countries. In other first legs, Algeria defeated Sierra Leone 2-0, Morocco edged Tunisia 1-0 and Zimbabwe and South Africa drew 1-1 in a competition restricted to under-23 footballers.
But the striker atoned three minutes after half-time when he poked a loose ball into the net after Mafoumbi failed to grasp a low Godwin Saviour cross. Rattled Congo were two goals behind six minutes later as Ajayi sneaked unnoticed into the six-yard box and nodded home a cross after Etor Daniel beat out-of-position Mafoumbi to the ball.
Nigeria attacked relentlessly, seeking more goals and a tie-clinching lead ahead of the early August return match in Atlantic city Pointe-Noire. Congo halved the deficit against the run of play as Nigerian goalkeeper Daniel Emmanuel cleared the ball with his leg and Nkounkou dashed in to score.
Zimbabwe were fortunate to escape with a draw after South Africa created more chances on an artificial Rufaro Stadium pitch in Harare. Keegan Dolly gave the visitors a 67th-minute lead that was cancelled when Walter Musona converted a penalty seven minutes from time.
Abdelhakim Amokrane scored twice within 21 minutes of the kick-off as Algeria achieved a convincing victory over Sierra Leone at Stade Mustapha Tchaker in Blida near Algiers. Far superior Morocco pipped Tunisia in Rabat thanks to an Achraf Bencherki penalty on the stroke of half-time at Stade Moulay Hassan.
The seven third-round winners advance to a tournament, held between 28 November and 12 December, with hosts Senegal and the top-three finishers qualifying for Rio 2016.