The sixteen teams were drawn into four groups of four. Each group contained two of the seeded teams, and two teams that had advanced from the first round. The teams would play against each other on a home-and-away basis. The four group winners advanced to the Final Round .
Group A
Libya withdrew after playing their first group match; their second game was originally awarded to opponents Algeria by walkover, but all Libyan results were later annulled by FIFA .
6 January 1989
Attendance: 50,000
Referee: Mohamed Hafez (
Egypt )
8 January 1989
Attendance: 30,032
Referee: Simon Bantsimba (
Congo )
22 January 1989
Attendance: 21,121
Referee: Bester Kalombo (
Malawi )
13 August 1989
Referee: Badou Jasseh (
Gambia )
Group B
7 January 1989
Referee: Hassan Abdulle Ahmed (
Somalia )
10 June 1989
Referee: Joel Dwarf Mondoka (
Zambia )
11 June 1989
Attendance: 28,000
Referee: Laryea Louis (
Ghana )
12 August 1989
Attendance: 55,000
Referee: Hassan Ahmed Abdulle (
Somalia )
12 August 1989
Attendance: 30,000
Referee: Mohamed Abdel Salam Gasmalla (
Sudan )
26 August 1989
Referee: Joel Dwarf Mondoka (
Zambia )
Group C
7 January 1989
Attendance: 50,000
Referee: Badou Jasseh (
Gambia )
8 January 1989
Attendance: 50,000
Referee: Dodji Hounnake-Kouassi (
Togo )
22 January 1989
Attendance: 60,000
Referee: Joel Mondoka (
Zambia )
10 June 1989
Attendance: 50,000
Referee: Mohamed Hossam El-Din (
Egypt )
25 June 1989
Attendance: 60,000
Referee: Simon Bantsimba (
Congo )
12 August 1989
Attendance: 100,000
Referee: Dodji Hounnake-Kouassi (
Togo )
Nigerian player Samuel Okwaraji died during this match.
Group D
8 January 1989
Attendance: 35,000
Referee: Bashir Salem (
Libya )
25 June 1989
Attendance: 40,000
Referee: Bester Kalombo (
Malawi )
13 August 1989
Referee: Mohamed Mohamed Hafez (
Egypt )
27 August 1989
Attendance: 1,839
Referee: Abderrahmane Bergui (
Algeria )