The 27-year-old forward headed powerfully past Uganda goalkeeper Denis Onyango off a cross from former Atletico Madrid youth squad member Robin Ngalande.
Richard Mbulu scored after 16 minutes to give Malawi a 1-0 Group B victory over Uganda on Monday, and qualification for the 2021 Africa Cup of Nations
It was the second time in six days that a goal from the South Africa-based attacker proved decisive as he also scored in last Wednesday's 1-0 win over South Sudan.
The son of a former footballer, Mbulu was based in Mozambique twice and Portugal before signing a three-year contract with South African Premiership club Baroka in 2019.
Hosts Malawi needed maximum points at Kamuzu Stadium in commercial capital Blantyre to secure a first appearance since 2010 while a draw would have sufficed for Uganda.
Victory temporarily took Malawi to the top of the table with 10 points -- they were overtaken three hours later when fellow qualifiers Burkina Faso defeated South Sudan 1-0 in Ouagadougou.
Aston Villa forward Bertrand Traore scored the Burkinabe goal on 50 minutes as the team finished unbeaten a six-match qualifying campaign spanning 17 months.
Popularly known as the Flames, Malawi are ranked 123rd in the world, 40 places below Uganda, and will be making a third appearance at the finals after first-round exits from the 1984 and 2010 editions.
They are the 19th qualifiers after Algeria, Burkina Faso, Cameroon, Comoros, Egypt, Equatorial Guinea, Gabon, Gambia, Ghana, Guinea, Ivory Coast, Mali, Morocco, Nigeria, Senegal, Sudan, Tunisia and Zimbabwe.
Joint leading Premier League scorer Mohamed Salah of Liverpool scored twice as Egypt netted four times in 10 minutes during the first half to hammer the Comoros 4-0 in Cairo and top Group G.
Kenya claimed a first win in the same section with goals from Hassan Abdallah and Masoud Juma, off a penalty, delivering a 2-1 win in Togo.
Captain Riyad Mahrez scored as Group H table-toppers Algeria finished with a 5-0 rout of Botswana in Blida, which stretched an unbeaten record in competitive and friendly matches to 24.
Zimbabwe, the other qualifiers from the section, fell 2-0 to neighbours Zambia in Harare with Patson Daka netting twice to become the leading scorer in qualifying with five goals.
Both Group D qualifiers lost with Gabon beaten 2-0 by Angola in Luanda and the Gambia going down 1-0 to the Democratic Republic of Congo in Kinshasa.
The remaining five places will be filled on Tuesday with the Central African Republic, who have never qualified for the premier African national team competition, among 12 hopefuls.
They host Mauritania in Bangui and a victory will take them to Cameroon unless Burundi achieve an unlikely away win over Group E winners Morocco.