The result saw the Ghanaian champions lose 4-1 on aggregate to the Congolese giants after Mazembe had secured a 1-0 victory in the first leg at the TnA Stadium last Sunday.
Medeama travelled to the Stade TP Mazembe needing to overturn the one-goal deficit but found themselves on the back foot early in the contest.
TP Mazembe took the lead in the 16th minute through Patrick Mwanungulu, who capitalised on the hosts' strong start to put Medeama under immediate pressure.
The home side doubled their advantage eight minutes later when Kazema Baso found the back of the net to give Mazembe a 2-0 lead on the night and put Medeama in a difficult position.
The Ghanaian champions struggled to find a response before the break as Mazembe maintained control and protected their two-goal advantage.
Mwanungulu then settled the tie in the 78th minute, scoring his second to make it 3-0.
Medeama found a consolation goal nine minutes later, with Dominic Amponsah pulling one back for the visitors in the 87th minute.
However, the goal came too late to spark a comeback as Mazembe held on for a 3-1 victory and progressed to the next stage with a 4-1 aggregate win.
The defeat brings an early end to Medeama's hopes of competing in the CAF Champions League this season.
The Ghanaian champions will now turn their attention to domestic football as they prepare to defend their Ghana Premier League title.
