Mozambique left it until the 89th minute to earn their first ever win over Chipolopolo with Germany-based Stanley Ratifo scoring the goal in Ndola.
2012 African champions Zambia dominated the Group K encounter for long spells but failed to turn their superiority into goals.
The Mambas made them pay for their profligacy when Ratifo finished brilliantly from a cut-back to stun the home side.
Elias Pelembe should have doubled the lead in added time but goalkeeper Kennedy Mweene rushed out of his box to stop the Bidvest Wits winger.
Coach Abel Xavier and the Mambas held on to celebrate a first triumph over Zambia in 18 attempts.
|Friday:||Grp L: Cape Verde v Uganda (1730)|
|Grp A: Sudan 1-3 Madagascar||Grp G: DR Congo v Congo (1730)|
|Grp E: Libya 5-1 Seychelles||Grp I: Burkina Faso v Angola (1800)|
|Saturday:||Grp C: Mali v Gabon (1900)|
|Grp B: Malawi 1-0 Comoros||Grp A: Senegal v Equatorial Guinea (2000)|
|Grp C: Burundi 3-0 South Sudan||Grp H: Ivory Coast v Guinea (2000)|
|Grp K: Zambia 0-1 Mozambique||Sunday:|
|Grp I: Botswana 0-1 Mauritania||Grp G: Zimbabwe v Liberia (1300)|
|Grp B: Cameroon 1-0 Morocco||Grp H: CAR v Rwanda (1400)|
|Grp J: Niger v Swaziland (1500)||Grp D: Benin v The Gambia (1500)|
|Grp K: Guinea-Bissau v Namibia (1600)||Grp F: Ghana v Ethiopia (1530)|
|Grp E: Nigeria v South Africa (1600)||Grp D: Algeria v Togo (2100)|
|Grp F: Sierra Leone v Kenya (1630)||Grp J: Tunisia v Egypt (2200)|
|Grp L: Tanzania v Lesotho (1700)|
The twelve group winners plus the best three group runners-up will qualify for the 2019 Africa Cup of Nations along with the hosts Cameroon.
Gerald Phiri Junior scored the only goal as Malawi began their Group B campaign with a home win over Comoros in Blantyre.
The South Africa-based winger hit a free-kick from outside the 18 yard box which flew over the wall and into the right corner on 31 minutes .
The flames had several chances but failed to punish a resolute Comoros.
It is a first competitive win for Malawi's coach Ronny Van Geneugden who took over in April.
Malawi have taken an early advantage in the group after hosts Cameroon beat Morocco 1-0 in Yaounde.
Vincent Aboubakar scored Cameroon's only goal in their 1-0 win over Morocco
A 29th minute goal from Vincent Aboubakar gave the Indomitable Lions the victory which puts Morocco bottom of Group B after the opening round of matches.
Cameroon qualify automatically as hosts for the 2019 Nations Cup, but their group matches still count as qualifiers for their opponents.
Burundi began their 2019 Nations Cup campaign in triumphant fashion by beating South Sudan 3-0 in Group C on Saturday.
The Swallows secured all three points with first half goals.
Cedric Amissi set the tone with the opening goal in the 15th minute.
Gael Duhayinnavyi added the second ten minutes later before Fiston Abdul Razak made it three in the 30th minute.
Mali face Gabon later on Saturday in the other Group C match.
Mohamed Abdellahi Soudani's second-half strike sealed a famous win for Mauritania away to Botswana.
The Mourabitones stunned the hosts in the 78th minute to go top of Group I.
Angola are away to Burkina Faso in the other group fixture.
On Friday, Libya and Madagascar opened the 2019 Africa Cup of Nations qualifying campaign with impressive victories.
Libya beat Seychelles 5-1 in Group A and in the first qualifier for Cameroon 2019, Madagascar were 3-1 winners away to Sudan in Al-Obeid in Group E.