Mali’s two quick goals and a late third were enough to sink Malawi – but not enough to ensure qualification.
Instead, Angola and Algeria went through after their 0-0 draw in Group A’s other game.
Frederic Kanoute put the Eagles ahead after just 40 seconds, and Seydou Keita struck with a fine free-kick moments later.
Malawi’s Russell Mwafulirwa pulled one back, but Mamadou Bagayoko made it 3-1 with five minutes left.
Mwafulirwa was left wondering what could have been as he sensationally missed the chance to make it level mid-way through the second half – his downwards header bouncing over the open goal.
The draw in Group A’s other game meant Angola won the group with five points, Algeria and Mali finish level on four points and Malawi bottom on three.
Under tournament regulations the head-to-head record between Algeria and Mali was used to decide who advances, rather than goal difference.
As news of the goalless draw filtered to the players in the stadium, Mali were unhappy with the outcome of the group.
“This is really disappointing,” said Bagayoko after the game.
“They changed the rules this year and we are out despite finishing ahead of Algeria [on goal difference].
“It’s a pity because we have a really talented bunch of players. We had the weapons to do something at this African Nations Cup.”
Mali took this game by the scruff of the neck early on.
A bizarrely calm clearance from goalkeeper Swadick Sanudi fell neatly to an alert Kanoute who fired the ball straight back to make it 1-0 within just 40 seconds.
The tournament’s quickest goal was followed by arguably its best two minutes later.
Seydou Keita hit a magnificent free-kick which flew over the wall, over the goalkeeper, and into the top left corner.
Admirably, Malawi began to get a grip on the game – certainly not looking like a side rocked by two early goals.
A good turn and shot from Joseph Kamwendo forced a solid save from Mahamadou Sidibe in the 24th minute, and Wadabwa could have scored two minutes later when he nudged a free header just over.
In the second half, Malawi adopted a more aggressive shape to chase the lead.
The pressure paid dividends when Mwafulirwa provided the final boot of a penalty area scramble to bring it to 2-1.
Mali should have been given a penalty 63 minutes in – Keita mercilessly taken down in the box but the referee played on.
In a moment that may haunt Mwafulirwa for months, he met Joseph Kamwendo’s cross from the left flank.
Rising well and above the ball, Mwafulirwa seemed to do everything right – only to see his header managed to hop over the bar.
Mwafulirwa almost made up for it with another header – this time on target – forced a good close-range save from Sidibe, only for the linesman to rule it offside anyway.
It was of little importance, however, as Mali went 3-1 up with five minutes remaining.
Mamadou Bagayoko met Modibo Maiga’s cross to head the ball, and the match, safely home.
Malawi can take pride in a campaign which saw them beat World Cup-qualifiers Algeria 3-0 in their opening game.
“We came as underdogs but the players fought in this tournament,” coach Kinnah Phiri said.
“In football we must accept defeat. We learned a lot throughout.”
Mali: Sidibe, Berthe, Abdallaye Maiga (Sow 50), Diamoutene, Tamboura, El Hadj Traore (Diallo 60), Fane, Mohamed Sissoko, Keita, Kanoute (Modibo Maiga 81), Bagayoko.
Subs Not Used: Diakite, Diarra, Ndiaye, Samassa, Soumare, Abdou Traore, Bakaye Traore, Yatabare, Oumar Sissoko.
Goals: Kanoute 1, Keita 3, Bagayoko 85.
Malawi: Sanudi, Mponda, Kafoteka (Chiukepo 52), Sangala, Chavula, Mwakasungula, Wadabwa (Nyondo 48), Kamwendo, Banda, Kanyenda (Ngambi 71), Mwafulirwa.
Subs Not Used: Nthala, Mgangira, Kamanga, Ngwira, Victor Nyirenda, Zakazaka, Msowoya, Harry Nyirenda, Swini.
Booked: Mponda, Banda.
Goals: Mwafulirwa 58.
Attendance: 21,000
Referee: Rajin Seechurn (Mauritius).
Other AFCON fixtures on 18 January
1996 Group: Cameroon 2-1 Egypt
1996 Group: Algeria 2-0 Sierra Leone
2010 Group: Angola 0-0 Algeria
2015 Group: Zambia 1-1 DR Cong0
2015 Group: Tunisia 1-1 Cape Verde
2017 Group: Gabon 1-1 Burkina Faso
2017 Group: Cameroon 2-1 Guinea Bissau
By: George ‘Alan Green’ Mahamah
