Angola's low point came just after the hour when, trailing 1-0 but still on course to qualify, Dani Mussunguna tried to head the ball back to his goalkeeper but instead sent it over his head, leaving Wilfried Bony to tap into an empty net.
Emmanuel Eboue had put the Ivorians ahead after 32 minutes following another blunder at the back.
Angola, who were twice close to pulling a goal back, finished third in Group B with four points, losing out on goal difference to Sudan, who took second place with a 2-1 win over Burkina Faso.
Ivory Coast had already qualified and topped the group with maximum points from three games, which they completed without conceding a goal.
"We always put Angola first," said coach Lito Vidigal, who spent most of the news conference complaining about the standard of the translation from Portuguese to English, which was provided by a director of the Angolan federation.
"We had a lot of problems which I don't even want to talk about. My players did a fantastic job," added Vidigal, who pulled faces when his words were translated and complained they were being taken out of context.
NINE CHANGES
Ivory Coast made nine changes to the side that started the 2-0 win over Burkina Faso while Angola's ambitions were clearly limited to collecting the point they needed as they packed their defence.
On another steamy Malabo evening, the few first-half chances all fell to the Ivorians. Bony produced a run and powerful low drive which was well saved by Wilson Pereira and Kolo Toure drove a 35-metre shot narrowly wide following a free-kick.
Bony also had a helping hand in their first goal with a strong run down the left and low ball into the area. Angola defender Miguel Quiami appeared to have the ball covered but it slipped through his legs for Eboue to tap in at the far post.
With Sudan winning their game against Burkina, Angola looked increasingly edgy and they gifted Ivory Coast another goal.
In the 65th minute, Mussunguna got his head to Abdulkader Keita's long ball forward but sent his attempted clearance over the head of stranded Pereira and Bony tapped the ball into the empty net to take the credit for the goal.
Facing elimination, Angola came to life and were twice close to pulling back a goal which would have taken them through on goals scored.
Manucho had a powerful header brilliantly punched away from under the bar by Daniel Yeboah, then Kolo Toure hooked a goal-bound shot off the line.
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