The Senegalese Teranga Lions burst out of the blocks in the southeastern Gabonese city to score twice within 13 minutes through Mane and Henri Saivet.
Senegal are assured of topping Group B even if they lose their final match against struggling Algeria, and will tackle the Group A runners-up for a last-four place.
Gabon denied opening day win in African Cup of Nations
When Senegal face Algeria in Franceville next Monday, Tunisia will meet Zimbabwe in the Gabonese capital, Libreville.
Senegal have six points from two matches, Tunisia three and Algeria and Zimbabwe have one each going into the final round.
Senegal eye quarter-final berth
"The goal today was to qualify and we have done that," said Senegal coach and 2002 World Cup star Aliou Cisse. "Even when we played badly in the first match (against Tunisia), we won. Today we played well and won and we have qualified.
"It's been 10 years since we last made the quarter-finals. Now we have done it and I congratulate the players. I am very proud of the guys. Now we have to continue like this."
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