Both sides were guaranteed progression ahead of their clash in Kinshasa, but the hosts needed a win to usurp their Congolese rivals at the summit.
The spoils were shared at the Stade Tata Raphael, though, leaving them both on 11 points, with Mazembe's goal difference edging them ahead in the standings.
It means Vita take on CS Sfaxien rather than ES Setif in the semi-finals, with the Algerian side facing Mazembe next.
Sunday's later game was between Group B's bottom two - Es Tunis and Al Ahli Benghazi - who had no hope of making it through.
The two met at the Stade Olympique de Rades eager to avoid finishing bottom of the pile and, in a game lacking attacking quality, it was a penalty that proved decisive.
Es Tunis' Saif Jerbi was the man on target for the hosts 20 minutes from time as Khaled Ben Yahia's men moved off the foot of the group with their second win.
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