The Congolese needed a victory to qualify and they got off to a brilliant start when, seconds after Lomana LuaLua had hit the post, they were awarded a penalty thanks to a clumsy challenge from Momo Sissoko on Yves Diba.
Dieumerci Mbokani made no mistake from the spot, but Mali were level soon afterwards when Mamadou Samassa finished well after fine wingplay from left-back Adama Tamboura.
The promising start did not hold up, though, as the match descended into a scrappy game of cat and mouse and Congo played the more positive football, seeing three penalty appeals rejected, although Mali created the better chances on the counter-attack and twice hit the woodwork late on.
The draw was ultimately a fair result, although one that only suited Mali, who finish on four points, behind group winners Ghana, who breezed past Niger 3-0 to end on seven points.
Claude LeRoy's Congo, meanwhile, bow out with their heads held high having drawn all their matches, but they will look at the failure to beat Niger as a missed opportunity.
The match in Durban was always set to be a tense affair, with Mali feeling a sense of injustice after a hotly-disputed penalty saw them lose to Ghana in their last match.
The Congolese, meanwhile, had battled to a creditable draw with the Black Stars, only to draw 0-0 with minnows Niger, a result that ultimately proved their downfall.
A frantic start boded well as, from kick-off, LuaLua raced in down the left before curling a wonderful shot past Mali’s goalkeeper – also confusingly named Mamadou Samassa – but off the inside of the post.
Seconds later his side had a penalty as, with Mali failing to clear the loose ball, Diba skipped into the box, drawing a foul from Sissoko that was correctly penalised by the Algerian referee.
Anderlecht hit-man Mbokani stepped up and buried the spot-kick in the top right.
The joy was unbridled but brief, as Mali were level just over 10 minutes later. Tamboura, a constant threat on the left, had just seen a cross blocked but Congo failed to complete the clearance and the Denmark-based defender was able to send another ball into the box.
This time it landed at the feet of Samassa the striker, who drilled home a low finish through a crowd of bodies.
The rest of the first half was something of a dirge, the only moments of note when LuaLua saw a penalty claim rejected after a collision with Fousseni Diawara, while for Mali, Modibo Maiga headed over from a great position after a fantastic ball by Seydou Keita.
Initially, the second half was similarly cagey, with Mali aware that Ghana were comfortably leading Niger and thus happy to sit back and beckon Congo on to them.
Indeed, there were no clear-cut opportunities until the 66th minute, when Congo keeper Muteba Kidiaba nearly spilled a Samassa daisy-cutter into his own net, the eccentric TP Mazembe shot-stopper relieved to see the ball trickle wide.
The match had sparked back into life, with Congo’s West Brom midfielder Youssouf Mulumbu denied a long-range howitzer by Mali keeper Samassa’s low stop.
The latter stages saw Congo throw men and ball forward alike, but the overall impact was a series of opportunities for Mali on the break: Mohamed Traore headed off the outside of the woodwork, while towering striker Cheick Diabate also hit the post and was denied two headed goals by last-gasp interventions from Peterborough defender Gabriel Zakuani.
Congo, meanwhile, saw penalty appeals by Mbokani twice waved away, the Anderlecht striker once kicking his own foot and another time going down easily.
Mali’s talismanic skipper Keita nearly had the last word with a solo effort deep into injury time, but it would have been harsh on Congo who must now look to their World Cup qualification campaign – they lie second in Group I, behind surprise package Libya.
Mali, meanwhile, will hope to avoid the likes of Ivory Coast and hosts South Africa in the quarter-final draw, with Group C open and favourites Nigeria currently in third ahead of the final match.