Hamad Ahniash headed home from a corner in the last minute of the game to give Libya a dramatic 2-1 win over Cameroon to go top of Group I.
In Group F, stuttering start to their World Cup qualifying campaign continued on Saturday as they were held to a 1-1 draw away by Malawi.
Senegal also featured in a 1-1 draw with Uganda in a Group J clash in Kampala.
Midfielder Reuben Gabriel scored in second half stoppage time to seemingly again hand Nigeria a late victory for a second successive week, only for Malawi substitute John Banda to equalise a minute later.
It was a match in which the Flames outplayed their more illustrious visitors for long periods but were undone by poor finishing.
The Flames opened their group campaign with a goalless draw in Kenya last weekend, while the Super Eagles had to wait until the 80th minute before finding a way past a stubborn Namibia side.
Nigeria are unbeaten in World Cup qualifying since losing in Angola in 2004, but they struggled to impose themselves against the Malawians.
Nigeria, who have been to four of the last five World Cup finals, laboured again to add to the largely ineffective performance in Calabar last Sunday.
Despite the setback, the Super Eagles still lead the group because of Namibia's victory over Kenya in Windhoek on Saturday.
An 85th-minute goal from Henrico Botes secured maximum points for the hosts.
Egypt edged 10-man Guinea 3-2 on Sunday in a Conakry thriller to boost hopes of returning to the World Cup in 2014 after a 24-year absence.
Guinea led at half-time, had goalkeeper Naby Yattara red carded at 1-1, trailed and equalised before Mohamed Salah stunned the capacity 35,000 crowd at Stade du 28 Septembre with a late winner in the second round qualifier.
Veteran midfielder Mohamed Aboutrika scored twice within 10 minutes during the second half after Aboul Camara had given Guinea the lead and Alhassane Bangoura netted on 88 minutes to temporarily bring the teams level.
Although Egypt have lifted the Africa Cup of Nations a record seven times, they have qualified for the World Cup only twice - in 1934 and 1990 - and Bradley has repeatedly said that reaching Brazil is his primary objective.
The Pharaohs and the National Elephant look the strongest teams in a Group G completed by Mozambique and Zimbabwe, who played a goalless draw in Maputo.
Egypt have six points from two games, Guinea three and Zimbabwe and Mozambique one each and the North African team coached by American Bob Bradley hold the vital advantage of having played their most powerful foe away.
Mali bounced back from last weekend's defeat to Benin when they beat Algeria in neutral Ouagadougou on Sunday.
Goals from Mahamodou Ndiaye and Modibo Maiga carried the day for the Eagles.
Islam Slimani had given the Desert Foxes the lead who surrendered leadership of the group to Benin.
The game was moved to the capital of Burkina Faso given the recent political problems in Mali following the March coup.
Rwanda snatched a 1-1 Group H draw with improving Benin in Kigali, thanks to a late Labama Kamana goal from the penalty spot after Razak Omotoyossi had opened the scoring in the second half against the run of play.
The award of the spot kick two minutes from time angered Benin defender Khaled Adenon so much that he attacked the Ethiopian referee and after being red carded, was escorted from the pitch by police.
Avoiding defeat was a relief for Serbia-born Rwanda coach Milutin Sredojevic after the Wasps were badly stung in North Africa recently, conceding five goals against Tunisia in a friendly and four against Algeria in another qualifier.
Cameroon, whose six World Cup appearances is a record for an African country, suffered a dramatic 2-1 loss in Group I against Libya, who were forced to play in Tunisian city Sfax because of security instability at home.
Ahmed Zouay gave the Mediterranean Knights a quick lead at Taieb Mhiri Stadium, Eric-Maxim Choupo-Moting levelled and the winner came in the final minute when Mohamed Esnany nodded a corner past goalkeeper Carlos Kameni.
Defeat was a bitter pill for under-pressure Indomitable Lions coach Denis Lavagne to swallow as his team recovered from a sluggish start to dominate the second half but squander chances.
The DR Congo climbed above Cameroon on goal difference into second place behind Libya after a 2-0 win over Togo in Kinshasa despite playing more than half the game a man short because Albert Mutamba was sent off.
Congolese talisman Tresor Mputu scored midway through the opening half and Belgium-based midfielder Dieumerci Mbokani capped his return after a self-imposed 14-month exile by converting a late penalty.
New captain and Newcastle striker Papiss Cisse put the Teranga Lions ahead in the 37th.
But Godfrey Walusimbi eaqualised for the Cranes from the penalty spot.
The Cranes began their group campaign in fine style, scoring a late equaliser to grab an important point in Angola while Senegal defeated Liberia 3-1 on the opening day.
Liberia and Angola created few scoring chances during a drab 0-0 draw in Monrovia that benefited Senegal most as they lead Group J by two points.
Angola qualified for the 2006 World Cup against many expectations but struggled to make impression against a team that struggled to impress in recent years.