Shabani Nonda scored on his competitive return for DR Congo
Both DR Congo and Ghana lost the chance to make up ground on Group Two leaders South Africa when drawing 1-1 in Kinshasa on Sunday.
The result leaves both teams three points adrift of Bafana Bafana, who have 12 points from their six games.
With four matches of the qualifying series left, Cape Verde surprisingly sit in second place in the group - above both DR Congo and Ghana.
Group 3 standings after six games
South Africa - 12 points
Cape Verde - 10
Ghana - 9
DR Congo - 9
Burkina Faso - 6
Uganda - 4
The Black Stars had got off to the perfect start before a huge crowd in Kinshasa when Asamoah Gyan fired home following a goalmouth scramble after 31 minutes.
The match was the first competitive qualifier for new Ghana coach Ratomir Dujkovic, who would have been dismayed to see Shabani Nonda bring the Simbas level six minutes into the second half.
Nonda was making his competitive return for DR Congo after missing two years of international football through injury.
On Saturday, the Cape Verde Islands had kept alive their hopes of reaching a first Nations Cup finals with a key 2-1 victory in Burkina Faso.
Qatar-based Carlos Brito opened the scoring in the 53rd minute before the Burkinabes drew level through Moumouni Dagano in the 70th minute.
However, the Cape Verdians wrapped up victory with just two minutes remaining when Brito scored his second of the game.
South Africa's Quinton Fortune celebrates his goal against Uganda
The result means Cape Verde have ten points from their six matches, just two points behind South Africa.
Bafana Bafana also played on Saturday, maintaing their group lead with a 2-1 win over Uganda in Johannesburg.
The home side were gifted a 21st-minute penalty by Nigerian referee Chukwudi Chukwujekwu, who mysteriously pointed to the spot when there was no hint of a handball or foul.
Quinton Fortune asked no questions and netted emphatically from the spot.
The Ugandans continued to impress against a disjointed home side and were duly rewarded with an equaliser in the 65th minute when the impressive David Obua scored another penalty after Nasief Morris had fouled Suleiman Tenywa in the box.
Just as the Ugandans seemed on the verge of snatching a draw or even a shock win, Steven Pienaar scored a close-range winner in the 76th minute, capitalising on slack marking by the Ugandan defence.
The defeat leaves Uganda bottom of the table, struggling with just four points from their six games.