Putting the blame of the defeat, which leaves the defending African champion rooted to the bottom of Group A, angry Nigerians called for the sack of Coach Stephen Keshi, with the hashtag #KeshiOut becoming a hit on Twitter.
Keshi was the highest trending topic on Saturday evening according to @trendinaliaNG.
There were very few kind words for the ex-international as fans blamed him for everything from team selection to arrogance.
A goal from Bakri Almadina just before half-time gave Sudan a famous victory over an uncoordinated Nigerian team.
The Super Eagles desperately needed a win to kick-start their campaign, after suffering a shock 2-2 home defeat by Congo Brazzaville and an away draw with South Africa in their opening qualifying matches.
Keshi, who is working without a contract, suffered a blow before a ball had even been kicked when Victor Moses was forced to withdraw because of a thigh injury.
His recent comments about uninvited Villarreal forward Ikechukwu Uche also attracted harsh criticism from fans.
The loss to Sudan means that South Africa , who overcame Congo 2-0 in Atlantic city Pointe-Noire, go top of the standings, ending Congo’s 100% record.
Bafana Bafana struck a quick double early in the second half, Bongani Ndulula and Tokelo Rantie scoring a goal each in the space of two minutes, to clinch victory.