Harrison Afful put them in front in the 13th minute but the goal was cancelled out by Deo Kanda with 20 minutes to go. The build up to the game, which was played in front of a full house in the Rades stadium near Tunis, was marred by crowd trouble a few minutes before kick-off.
Police moved in to prevent the problems and the match got going only a few minutes late.
There was further trouble during the match and following the Mazembe equaliser, police forced large numbers of fans to leave the ground, even though the game was still being played.
Mazembe earn a prize of $1.5 million and will go to Abu Dhabi to take part in the Club World Cup next month. Mazembe will open their tournament in the Gulf state with a game against the Mexican champions, Pachuca.