Ivory Coast, runners-up to hosts Egypt in the 2006 African Nations Cup, were three goals ahead at the break after Arsenal defender Kolo Toure, PSV Eindhoven striker Arouna Kone and Lens forward Aruna Dindane all scored first half goals.
Kone went on to score a hat-trick in the match after converting twice in the second half to hand Gabon, 4-0 winners over Madagascar last month, a 5-0 thrashing.
Botswana and Burundi pulled off stunning results against their Group 2 rivals Egypt and Mauritania respectively over the weekend.
Botswana held current Nationas Cup champions Egypt to a 0-0 draw at the National Stadium in Gaborone on Saturday, while Burundi notched up their first win with a surprising 3-1 result over Mauritania at the Stade Prince Louis Rwagasore in Bujumbura on Sunday.
Middlesbrough striker Yakubu Aiyegbeni ensured Nigeria remained undefeated at the top of Group 3, with a 50th minute strike against Lesotho at Setsoto National Stadium, Maseru.
The Super Eagles now have two wins from as many matches, and lead Uganda who drew 0-0 with Niger at the Général Seyni Kountché Stadion, Niamey on Sunday.
Cameroon were missing African Footballer of the Year Samuel Eto'o through injury, but replacement striker Idrissou Mohammadou did the job for the Indomitable Lions, scoring two late goals in a 3-0 win over Equatorial Guinea in their Group 5 match in Yaounde.
In Group 11, South Africa captain Aaron Mokoena scored the only goal in his side's 1-0 triumph over Zambia in Lusaka.
The Blackburn player put South Africa level on points with Congo after two matches.
All 12 group winners will advance to the biennial tournament of African football along with the three best runners-up from the 10 four-team pools. Ghana qualify automatically as hosts.