Debutant Afriyie Acquah's early goal ensured Ghana became the first side to qualify for the 2013 African Cup of Nations.
Ghana went into the match with a 2-0 advantage from the first leg, and Acquah's strike after just two minutes ensured the four-time champion will be present in South Africa early next year.
Mali delivered a firm statement of its abilities as the side thrashed Botswana 4-1 in Gaborone, meaning the side qualifies on an aggregate score of 7-1, but defending champion Zambia required a penalty shootout to progress at the expense of Uganda.
Zambia held a 1-0 advantage going into the second-leg clash in Kampala, but Geoffrey Massa's first half strike drew the host level in the tie, which went to a penalty shootout after 90 minutes.
The visitor won the 2012 Cup of Nations in a dramatic shootout against Cote d'Ivoire, and held its nerve again to beat Uganda 9-8 and book its place in next year's finals, to be held in South Africa.
Mali led 1-0 at the break, but underlined its dominance with three second half strikes, before Botswana claimed a late consolation goal.
Two-time champion Nigeria, which failed to qualify for the 2012 finals, ensured that it will return in 2013, after thumping a hapless Liberia 6-1 in Calabar.
A 2-2 draw in the first leg had left the tie finely balanced, but first half goals from Efe Ambrose and Ahmed Musa put Nigeria in charge before the host ran riot in the second half.
Chelsea's Victor Moses grabbed a second half brace, while John Obi Mikel and Ike Uche also scored for Nigeria.
Liberia aptain Gebro Duncan was sent off and Patrick Wleh's late goal was the only bright spot for the visitor.