Guinea finished second in group A, one point ahead of the east Africans, after Aboubacar Titi Camara equalised in the 84th minute with his third goal in as many games.
Tunisia, who went ahead with a superbly-taken Slim Benachour goal, had already qualified with a game to spare.
Debutants Rwanda, who lost 2-1 to Tunisia and then scored an injury-time equaliser to draw with 1-1 Guinea, chalked up their first win thanks to Said Abed Makasi’s 74th-minute goal in the Mediterranean port of Bizerte.
The defeat completed a disastrous tournament for the Simbas, who went home without a point after losing all three group games, and prompted coach Mark Wadsworth to criticise Congolese officials.
“The amount of pressure the players have to put up with from politicians and the federation is intolerable and unacceptable,” said the Englishman, who quits today after a brief two-month contract.
“They have spent more time talking to my players than me. Even at half-time today, I had to put up with a delegation of politicians that came in to address the players.”
Rwanda, who qualified at the expense of four-times champions Ghana just nine years after genocide killed hundreds of thousands in the country, held on as Kabamba Musasa twice headed against the woodwork in a match peppered with schoolboy errors.
Nigeria showed no ill-effects from their off-the-field drama as they recorded an emphatic 4-0 victory over South Africa in Group D.
The Super Eagles’ preparations for this crucial match, which they had to win after they lost to Morocco, were thrown into disarray after three key players were told to leave the squad due to indiscipline.
Chelsea’s Celestine Babayaro, Portsmouth’s Aiyegbeni Yakubu and Schalke’s Victor Agali were all axed from the team camp at Monastir.
Despite those absences Nigeria took the lead after just four minutes when South Africa goalkeeper Emile Baron flapped at a corner and Everton defender Joseph Yobo stabbed the ball past three defenders on the line.
But Nigeria had to wait until the 64th minute until extending their advantage. Bolton midfielder Jay-Jay Okocha scored it, the competition’s 10,000th goal, from the penalty spot after Aaron Mokoena had handled just inside the area.
Peter Odemwingie, a substitute for Arsenal striker Kanu, then netted two late goals.
In the evening game, a below-par Morocco moved top of the group above Nigeria with a less-than-comfortable 4-0 win over Benin in Sfax. advantage until 17 minutes from time.