Alain Giresse’s men came into the game needing a win to stand any chance of progressing to the knockout stages, but as it turned out they would have crashed out regardless of their result after Egypt beat Ghana in the pool’s other game.
Neither goalkeeper had a save to make in a first half which saw the two teams – who had both failed to score in each of their first two games – struggle to cope with extreme wet conditions.
But the sides exchanged superb goals after the break, Faruku Miya’s powerful strike for Uganda cancelled out by a brilliant free-kick from Yves Bissouma.
There were no major chances for a winner, though, and both nations will watch the rest of the competition from home.
Mali finished third in the 2012 and 2013 AFCON tournaments, but have now exited at the group stage twice in a row.
Uganda were already eliminated going into the final matchday and end the event with just one point after qualifying for the first time since making the final back in 1978.
Mali threatened first with Moussa Marega shooting against the side netting after Molla Wague had headed into his path.
Uganda were then in on goal after Miya’s impressive throughball released Luwagga Kizito, but the ball was caught up in a puddle as the Rio Ave attacker prepared to shoot, denying him the chance to test Oumar Sissoko.
Mali came close at the other end when captain Yacouba Sylla curled inches over with an effort from 20 yards as a poor first half ended without a goal.
Kalifa Coulibaly failed to trouble Robert Odongkara with a header from Moussa Doumbia’s cross as the second half started at an even slower pace.
Uganda thought they had opened the scoring, but the assistant’s offside flag was raised after Khalid Aucho’s shot deflected in off Kizito, who had strayed past the last defender.
But Uganda were not to be denied and they soon took the lead in stunning fashion, scoring with the match’s first shot on target after 70 minutes.
Miya received Denis Iguma’s pass and took one touch before rifling an unstoppable effort past Sissoko from the edge of the area.
Mali then produced an even better response three minutes later, Bissouma unleashing a magnificent free-kick from 30 yards into the top corner, leaving Odongkara rooted to his spot.
Giresse’s side pressed for a winner but stretching substitute Mustapha Yatabare struck over with their best chance as they failed to trouble Odongkara and exited the competition.
Powered By:unibank Ghana Limited