Emmanuel Eboue scored in the 32nd minute and Wilfried Bony added a second in the 64th as cup favorite Ivory Coast sealed a third straight victory and first place in Group B.
The result meant Sudan progressed in second place on goal difference after beating Burkina Faso 2-1 in the other group match. Burkina Faso was already out.
Angola had needed only a draw to guarantee progression.
Ivory Coast, which made nine changes to its starting lineup against Angola, will play co-host Equatorial Guinea in the last eight, while Sudan will play Zambia.