
The minnow joined the ranks of international football in 2012 and had not found the net since a 3-1 defeat to Kenya in November 2013, but Atak Lual's 52nd-minute strike was enough to seal a 1-0 win in Juba.
The momentous result lifts Lee Sung-Je's side to second place in Group C ahead of Benin’s clash with Mali later this weekend.
There was similar joy for Liberia, which shocked Group A rival Tunisia with a 1-0 victory despite being without first-choice goalkeeper Nathaniel Sherman, who reportedly suffered a serious eye injury after inadvertently barging into a glass door at the team's hotel.
But a Francis Forkey Doe strike in the 11th minute proved decisive, in the first international match to be held in Monrovia since the lifting of the Ebola ban.
A late free-kick from Wakaso Mubarak made it two wins from two for Ghana in Group H as it beat Rwanda 1-0 away from home.
Avram Grant's side had begun its campaign with a 7-1 win over Mauritius but was frustrated by Rwanda for much of the match.
Ghana - runner-up to Cote d'Ivoire in 2015 - struggled to create chances on a dreadful pitch at the Stade Amahoro in Kigali before Wakaso curled home the winner from the edge of the area two minutes from time.
Grant's side will resume its bid for qualification in March with a two games against Mozambique.
Morocco was more emphatic in securing its second win in Group F, brushing aside Sao Tome e Príncipe 3-0.
In Group K, Senegal took advantage of Burundi's 2-0 win over Niger with 2-0 win away to Namibia, courtesy of goals from Premier League stars Cheikhou Kouyate and Sadio Mane – a win that leaves it three points clear at the top.
Sunday Oliseh's first game in charge of three-time champion Nigeria will not live long in the memory as Tanzania deservedly secured a goalless draw in a Group G clash at Benjamin Mkapa National Stadium.
Oliseh was charged with the task of replacing Stephen Keshi in July and the former Nigeria captain would have been expected to see off the minnow of Tanzania in his maiden competitive game at the helm.
As it was he was indebted to an assured display by debutant Carl Ikeme, starting after captain Vincent Enyeama withdrew from the squad after the death of his mother, for pulling off some vital saves to deny the host its first win over Nigeria.
Nigeria also had its chances to make it two qualifying victories out of two, but had to settle for a point in Dar es Salaam against a Tanzania side showing plenty of promise under a new coach of its own in Boniface Mkwasa.
Oliseh would have seen plenty of room for improvement from a youthful Nigeria side as he attempts to guide his country to the 2017 Cup of Nations in Gabon, having failed to qualify for this year's tournament in Equatorial Guinea earlier this year.
Nigeria though could be knocked off the top of Group G should Egypt beat Chad later this weekend.
South Africa's qualification hopes are hanging by a thread after it suffered a shock 3-1 Group M defeat at the hands of Mauritania.
Having been held to a 0-0 home draw by Gambia in its first qualifier, the pressure was on the visitor to get its campaign back on track with a victory over the unfancied host in Nouakchott.
But instead it fell behind as early as the sixth minute when goalkeeper Itumeleng Khune fumbled Aly Abeide's free-kick into the net.
South Africa then lost Siyabonga Zulu to a straight red card early in the second half after the debutant was deemed to have committed a professional foul, but still managed to get itself back on level terms on 68 minutes.
Anele Ngcongca provided the cross and the lively Thamsanqa Gabuza got in front of the home goalkeeper to nod home.
That proved to be a temporary reprieve for Shakes Mashaba's men, however, as Boubacar Beyguili restored Mauritania's lead on 79 minutes and Moulaye Ahmed sealed a famous victory for the host with a superb solo effort four minutes from time.
Mauritania has never qualified for the Cup of Nations, but is now in serious contention to emerge from Group M, especially as it hosts struggling Gambia next.
South Africa, meanwhile, faces the daunting prospect of having to take three points from March's trip to Cameroon if it is to stand any chance of making it to the finals in Gabon.
And it may well head into that game under a new coach with the pressure on Mashaba sure to increase in the wake of this latest setback.
A solitary 25th-minute strike from Tonny Mawejje saw Uganda rise to the top of Group D with a 1-0 win away to Comoros, overtaking Burkina Faso, which slumped to a 1-0 defeat at Botswana.
Elsewhere, 10-man Seychelles lifted itself off the bottom of Group J with a 1-1 draw to Ethiopia, while Group E remains wide open after Congo's 1-1 draw with Guinea-Bissau.
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