The victory was well-deserved as they had the better chances in the game, but were also frustrated for long periods by a resilient Lesotho side.
Lesotho opened the scoring on nine minutes when Taemane Shea headed home from a Moqolisi Mothae corner in a goal that came somewhat against the run of play.
Angola launched wave after wave of attacks on the Lesotho goal but it took until injury-time in the first half for them to find their equaliser.
Angola captain Manuel Manjolo launched a long ball to Valdemiro Domingos, who drilled his shot in at the far post.
The defending champions should have taken the lead when they were awarded a penalty, but Valdemiro Domingos’ shot was expertly saved by Lesotho goalkeeper Motlatsi Sebapala.
However, two goals in three minutes shortly afterwards sealed the points for the Angolans.
Rivaldo Fonseca bundled the ball in from a corner on the hour-mark, before substitute Francisco Chiquinho collected a pass from Osvaldo Inga and provided a neat finish.
The other match in Group B finished 0-0 between Mozambique and Comoros despite both teams having a number of chances to win the game.
After a goalless first half, Comoros captain Kamal Kifli had perhaps the best chance of the game when he found himself with an opportunity to shoot at goal, but instead opted to look for a pass and could not pick out a teammate.
Group A will be back in action on Monday when South Africa seek to kick-start their tournament against powerful Zambia.
South Africa lost their opener 3-0 to hosts Malawi, while Zambia brushed aside Eswatini in their first game to suggest they should be heavy favourites for this one.
The match will take place at the Mpira Stadium and kick-off is 11h00 local time (09h00 GMT).
The second game of the day sees Malawi tackle Eswatini, where they can take a giant step towards the semifinals with another win.
Malawi are hoping for their second title after lifting the trophy in 2001, and have so far been roared on by an enthusiastic crowd in Blantyre. This match kicks off at 14h00 (12h00 GMT)
Angola 3 (Domingos 45’, Fonseca 60’, Chiquinho 63’) Lesotho 1 (Shea 9’)
Mozambique 0 Comoros 0
11h00: South Africa vs Zambia – Mpira Stadium
14h00: Eswatini vs Malawi – Mpira Stadium
Group A P W D L GF GA Pts
Zambia 1 1 0 0 6 0 3
Malawi 1 1 0 0 3 0 3
South Africa 1 0 0 1 0 3 0
Eswatini 1 0 0 1 0 6 0
Group B P W D L GF GA Pts
Comoros 2 1 1 0 1 0 4
Mozambique 2 1 1 0 1 0 4
Angola 2 1 0 1 3 2 3
Lesotho 2 0 0 2 1 4 0
Matches Played: 6
Goals scored: 15
Biggest victory: Zambia 6 Eswatini 0 (Group A, October 12)
Most goals in a game: 6 – Zambia 6 Eswatini 0 (Group A, October 12)
2 goals – Dave Tobias (Malawi)
1 – Francisco Chiquinho (Angola), Miguel Chirwa (Zambia), Valdemiro Domingos (Angola), Rivaldo Fonseca (Angola), Julius Kumwenda (Zambia), Kamal Kifli (Comoros), Moses Mulenga (Zambia), Charles Mumba (Zambia), Rickson Ng’ambi (Zambia), Taemane Shea (Lesotho), Chipyoka Songa (Zambia), Mike Thomu (Malawi), Aylot Zerefos (Mozambique)