Tunisia finish top of Group B with five points from three games, while Congo DR join them thanks to the fact that they have scored one more goal than Cape Verde, who were only able to draw 0-0 with Zambia in tonight's other game.
Chikhaoui's shot at goal was turned home by strike partner Ahmed Akaichi, giving Muteba no chance of keeping it out.
In the second half both Akaichi and Wahbi Khazri had golden opportunities to double Tunisia's lead, but they were unable to take them and Congo DR punished them.
Six minutes after coming on as a substitute, Jeremy Bokila prodded home from close range to score the crucial goal Congo DR needed to book their place in the last eight.
Congo DR would have won the group with another goal, but it was Tunisia who went closest to victory on the night when Hamza Younes was denied by the gloves of Muteba.