Substitute Nnamdi Oduamadi, who plays for Italian second-tier club Varese, scored three minutes into stoppage time to save the Nigerians from an embarrassing defeat.
Francis Kahata had put Kenya ahead with a curling free kick in the first half.
It was the second draw in three games for Nigeria who have five points, level with Malawi at the top of the group. Namibia have three points from three matches and Kenya are bottom on two points.
The match was Nigeria's first since their success at the Nations Cup. They have five points from three games, level at the top of Group F with Malawi who beat Namibia 1-0 in Windhoek.
A curling free kick by Francis Kahata put Kenya ahead before halftime in Calabar. The equaliser came from a long throw as a desperate Nigeria threw everything forward.
Samuel Eto'o scored twice to lead Cameroon to a 2-1 victory in Yaounde against Togo who were without Tottenham Hotspur striker Emmanuel Adebayor.
Captain Adebayor, involved in an on-off spat with coach Didier Six, did not play after failing to show up at Togo's training camp during the week.
Cameroon, aiming to qualify for Brazil 2014 after missing out on the last two Nations Cup tournaments, are top of Group I with six points from three games following victory over Togo.
The role of Eto'o was the subject of media speculation before the game but his two goals restored his status as leader of the team.
Wilfried Bony (penalty), Yaya Toure and Salomon Kalou struck as Ivory Coast defeated Gambia 3-0 without Galatasaray forward Didier Drogba, who was left out of the squad for the Group C encounter in Abidjan.
The Ivorians are top with seven points, four ahead of second-placed Tanzania who have a game in hand.
Tunisia maintained their 100 percent record in Group B by beating Sierra Leone 2-1.
The Tunisians have nine points from three games, five ahead of second-placed Sierra Leone.
Queens Park Rangers defender Christopher Samba, playing his first competitive game for Congo after a lengthy break from international football, notched the only goal in a 1-0 win over Gabon that put his team in a strong position in Group E.
Congo have nine points after winning all three of their qualifiers.
Second-placed Burkina Faso continued the form that took them to the Nations Cup final in February by hammering Group E rivals Niger 4-0 in Ouagadougou.
It was their first win of the campaign and they have much to do to stand any chance of progressing to the final round playoffs at the end of the year.
Senegal, top of Group J, suffered a surprise setback as they were held 1-1 by Angola who are second.
Moussa Sow gave the Senegalese a first-half lead in neutral Guinea before Amaro equalised with 15 minutes to go for the injury-hit Angolans.
The game was played in neutral Guinea after Senegal were banned for a year from playing at home following violent scenes in Dakar in October during a Nations Cup qualifier with Ivory Coast.
South Africa, who hosted the last World Cup in 2010, are on track to qualify for next year's edition in Brazil after beating Central African Republic 2-0 in a Group A tie.
Full-back Thabo Matlaba drove in a long-range shot in the 33rd minute before a second-half goal by Bernard Parker pushed the home team to the top of the group with five points from three matches.
The two countries meet again in Bangui in June.
Ethiopia, who have four points, can go back to first place if they beat bottom team Botswana in Addis Ababa on Sunday. Central African Republic are third with three points.
Nine more matches will be played across Africa on Sunday and a further two qualifiers are due to be staged on Tuesday.
AFRICAN WORLD CUP QUALIFYING RESULTS
South Africa 2-0 Central African Republic
Tunisia 2-1 Sierra Leone
Ivory Coast 3-0 Gambia
Congo 1-0 Gabon
Burkina Faso 4-0 Niger
Namibia 0-1 Malawi
Nigeria 1-1 Kenya
Cameroon 2-1 Togo
Senegal 1-1 Angola