Sudan stunned Africa Cup of Nations title-holders Nigeria 1-0 Saturday in a 2015 qualifier while Algeria, Ivory Coast and South Africa achieved impressive away victories.
Algeria overcame Malawi 2-0, South Africa triumphed by the same score in Congo Brazzaville and Ivory Coast won 2-1 in the Democratic Republic of Congo.
Sierra Leone exceeded expectations to hold Cameroon 0-0 in Yaounde after surrendering home advantage because of the Ebola epidemic and Togo upset Uganda 1-0 in Kampala.
The qualifiers took place amid a demand from 2015 hosts Morocco that the January 17-February 8 tournament be postponed over the Ebola crisis.
But the African Football Confederation (CAF) insisted Saturday that the three-week championship will go ahead as scheduled.
More than 4,000 people had died from the virus this year, according to the World Health Organisation, with virtually all the victims living in west African countries Guinea, Liberia and Sierra Leone.
A Bakry Almadina header on 41 minutes in Khartoum gave Sudan a first Group A win and Nigeria slumped to bottom place with a solitary point halfway through the qualifiers.
Chelsea midfielder John Obi Mikel netted three minutes from time but was clearly offside and he pulled another shot wide as the Super Eagles mounted a late offensive.
Sudan are 34 places below Nigeria in the African rankings and started the match as rank outsiders after being well beaten by South Africa and Congo Brazzaville last month.
South Africa made it three wins from five visits to Atlantic city Pointe-Noire by netting twice within four minutes soon after half-time.
Bongani Ndulula silenced a 15,000 crowd crammed into the Stade Municipal by scoring via a bicycle kick on 52 minutes.
Tokelo Rantie doubled the lead with a close-range shot after a superb pass from fellow England-based professional Dean Furman.
South Africa captain Senzo Meyiwa then made a string of saves to keep Congo at bay and when the Red Devils did score during stoppage time, the effort was ruled offside.
Defenders scored both Algerian goals in Blantyre with Rafik Halliche putting the Desert Foxes ahead on 10 minutes and substitute Djamel Mesbah adding a second in stoppage time.
Halliche nodded a corner past goalkeeper McDonald Harawa and Mesbah scored with a deflected close-range shot for the top-ranked team in Africa.
Algeria did best of the five African qualifiers for the 2014 World Cup in Brazil, taking eventual champions Germany to extra time before suffering a 2-1 loss.
Wilfried Bony from English Premier League outfit Swansea fluffed a penalty for Ivory Coast, then scored to give the Elephants a half-time lead in Kinshasa.
Cedric Mongongu levelled off a spot kick only for Max-Alain Gradel to earn the Ivorians maximum points with a goal seven minutes from time.