Tunisia guaranteed top spot in World Cup qualifying Group A and secured their ticket to Russia despite being held 0-0 at home by Libya on Saturday.
The Eagles of Carthage headed into their final fixture knowing that they would definitely reach the World Cup if they avoided defeat, but were frustrated by their neighbours.
They enjoyed 71 percent of the possession, but their finishing was profligate and they were unable to secure the goal that may have killed off the visitors' resolve.
Tunisia's point ensures their fifth World Cup participation -- and their first since 2006 - but ensures that the Democratic Republic of Congo's wait to return to the global showpiece for the first time since 1974 will continue.
The Leopards knew that they needed to beat already eliminated Guinea and hope that Libya downed Tunisia to overhaul the Eagles to top spot.
Florent Ibenge's side made hard work of the West Africans, and only opened the scoring in the 62nd minute when Ousmane Sidibe put the ball past his own goalkeeper.
Guinea levelled the contest in the 71st minute through Karamokoba Keita, but two goals in stoppage time - Neeskens Kebano's strike and a Jonathan Bolingi penalty - secured a 3-1 victory for the hosts.
The win takes Congo up to 13 points, but Libya's failure to beat Tunisia means they end the campaign tantalisingly one point short of the North Africans.
Ibenge's side will look back at their double header against the Tunisians, when they enjoyed the better of both contests but only took one point out of a possible six, as the reason why they will be watching on from the outside next summer.