The Southern African nation, with a population of just over two million, made sure of one of the two berths from Group K as they kept up their unbeaten run in the qualifiers.
They are the first side to emerge from the preliminaries, which only reached the halfway stage this weekend and join co-hosts Equatorial Guinea and Gabon in the 2012 field.
Striker Jerome Ramatlhakwane, who has not played club football for more than a year, kept up his goal-scoring run in the qualifiers with a second-half winner. It was his fifth goal in six games.
But while Botswana emerge onto the continent's top stage, defending champions Egypt and former winners Cameroon face the stark reality of missing out.
Both lost away on Saturday to injury-time goals with Egypt beaten by the last kick of the match against South Africa in Johannesburg and Cameroon going down to Senegal.
Katlego Mphela scored three minutes into additional time to give South African a fortunate 1-0 home win after Egypt had proved stronger and created the better chances.
But the north Africans, who have won the last three Nations Cup titles, remain winless and bottom of Group G, six points behind the South Africans.
Demba Ba's injury-time goal for Senegal in Dakar made it three wins out of three as the 2002 World Cup quarter-finalists continued their dramatic revival of the last nine months.
Cameroon, whose captain Samuel Eto'o was winning his 100th cap, are five points behind the pace in Group E.
Late goals also ensured 2-1 victories for Kenya over Angola and Tanzania against the Central African Republic.
East African success was complete when David Obua won the game for Uganda away in Guinea Bissau with the only goal of the Group J encounter.
Both Burkina Faso and the Cape Verde Islands strengthened their chances with handsome home wins. Burkina Faso trounced Namibia 4-0 while the Cape Verdians beat Liberia 4-2.
