Malawi's victory over the World Cup qualifiers in Luanda was followed by a similarly surprising showing from Burkina Faso, who held pre-tournament favourites Ivory Coast to a goalless draw in Cabinda.
Togo were officially disqualified after the scheduled kickoff time of their Group B match with Ghana, which did not take place because of the departure of the Togolese from the tournament some 24 hours earlier.
Togo's team had spoken of hoping to return after leaving Cabinda in the wake of Friday's bus attack that killed two of their delegation.
But the Confederation of African Football ruled on Monday evening that they were no longer in the tournament after forfeiting their match against Ghana.
It leaves the group a three-team affair with the position of the Ivorians precariously placed after they failed to break down a stubborn Burkinabe defence.
Cabinda's new Chiazi stadium was largely empty, amid tight security, as Didier Drogba and his much-vaunted team-mates squandered several chances.
The Ivorians had scored eight goals in two World Cup qualifiers against Burkina Faso in the preceding six months but said they expected their opponents to be much more defensive this time.
Malawi's triumph was emphatic and will have left Algeria's World Cup finals opponents, including England, far from convinced about the north Africans' ability to be competitive in South Africa in six months' time.
Russell Mwafulirwa took advantage of a fortunate rebound to score after 17 minutes before defender Elvis Kafoteka powered home a header nine minutes before halftime.
Soon after the interval, Davi Banda added a third, albeit injuring himself in the process and having to leave the field.