Substitute Nnamdi Oduamadi scored three minutes into stoppage time to snatch a 1-1 draw for the newly crowned African champions at home to Kenya in a surprise setback just six weeks after winning the Nations Cup.
Nigeria, who have only one home game left in Group F, share top place in their group with Malawi, who beat Namibia 1-0 away in Windhoek.
A curling free-kick from Francis Kahata put Kenya ahead before half-time in Calabar. Nnamdi's equaliser came off a long throw as desperate Nigeria went in search of a draw.
Samuel Eto'o scored twice to hand Cameroon a 2-1 win over Togo in Yaounde, as they seek to restore lost lustre after missing out of the last two Nations Cup.
CLICK HERE for our 2014 World Cup qualifier site to get the latest results and tables.
Eto'o's role in the side had been the subject of much conjecture before the game after he failed to turn up for a warm-up friendly last month.
But while he restored his status as leader of the team, Togo played without Emmanuel Adebayor who did not arrive for the game in a continuation of his spat with coach Didier Six.
Yaya Toure and Salomon Kalou were among scorers for the Ivory Coast as they beat the Gambia 3-0 at home without Didier Drogba, dropped for the Group C encounter in Abidjan.
Tunisia won a third game in Group C by beating Sierra Leone 2-1 at home to go well clear in their standings.
Giant defender Christopher Samba, playing in his first competitive game for Congo after a lengthy hiatus from international football, got the only goal in a narrow win over Gabon that puts them in a strong position in Group E.
Tunisia and Congo are the only teams so far with nine points from their first three qualifiers.
Burkina Faso continued the form that took them to the Nations Cup final in February by hammering Niger 4-0 at home in Ouagadougou. But it was their first success of the campaign and they are left with much to do if they are to stand any chance of progressing to the final round play-offs at the end of the year.
South Africa won their first Group A game by beating the Central African Republic 2-0 in Cape Town but Senegal suffered a surprise setback after being held 1-1 by Angola.
Moussa Sow gave them a first half lead in neutral Guinea, where the match was moved after Senegal were banned for a year from hosting home matches, but Amaro equalised 15 minutes from time for the injury-hit Angolans.
Meanwhile on Sunday, Zambia and Morocco were left to both reassess their World Cup qualification ambitions after setbacks put their campaigns in peril and made hollow predictions of a rise in their immediate fortunes.
Zambia extended to seven matches their winless streak as plucky Lesotho grabbed a late equaliser in a 1-1 draw in Maseru while Morocco crashed to a 3-1 defeat in Tanzania to fall well behind the Ivory Coast in their group standings.
Cape Verde Islands, the toast of the recent African Nations Cup with their surprise quarter-final place, crashed back to earth with a 4-3 defeat at Equatorial Guinea while the Democratic Republic of Congo were held at home by strife-torn Libya on a day the minnows came to the fore.
Zambia were African Nations Cup winners in 2012 and have made much of an experienced generation kicking on to secure a first ever World Cup place in Brazil.
But they have ceded advantage in Group D to Ghana, who beat Sudan 4-0 in Kumasi on Sunday.
Zambia still lead Ghana by a single point but have an away match in Ghana to come at the end of the group phase in September and coach Herve Renard said afterwards he feared the points dropped to 166th-ranked Lesotho could come back to haunt them.
A rasping left footed shot from long range from Litsepe Marabe saw unfancied Lesotho grab a dramatic late equaliser after Collins Mbesuma had out the 10-man Zambia side ahead with a quarter-hour left.
Zambia played almost the entire second half down to 10 men after goalkeeper Kennedy Mweene was sent off for a professional foul.
Morocco would need a minor miracle to revive their fortunes in Group C after their foreign-based do of Thomas Ulimwengu and Mbwana Samata (2) scored in a shock win in Dar-es-Salaam.
Morocco had spent the week training in Dubai for the game but could only muster a stoppage time consolation goal from Youssef Al Arabi.
Their much-vaunted squad has been consistently tipped to offer Morocco a chance to achieve on the African stage but the last 18 months have been filled with a series of setbacks.
Tanzania now move one point behind the Ivorians in the group but Morocco are five off the pace with three games left, including a trip to Abidjan.
DR Congo had a chance to join Cameroon atop Group I but played out a goalless draw with Libya, whose players mainly come from home-based clubs who have been without league action for two years now.
Cape Verde lost a third qualifier and are almost certainly out of the running after Emilio Nsue scored a hat trick on his debut. The Mallorca striker only agreed to play for Equatorial Guinea after failing to make Spain's squad for last year's Olympic Games football tournament.
Ethiopia went to the head of Group A after an 88th minute goal from Getaneh Kebede gave them a 1-0 home win over Botswana while Mali top Group H after coming from behind to Rwanda 2-1 away.
Two more African qualifiers are due on Tuesday when Egypt host Zimbabwe and Benin visit Algeria.
CLICK HERE for our 2014 World Cup qualifier site to get the latest results and tables.