Mazembe went to the return leg leading by a single goal after securing a 2-1 first-leg win away from home, as two goals from Mbwana Samatta and Roger Assale helped the Congolese giants prevail 4-1 on aggregate.
An ugly scuffle near the end of the match saw USM Alger's Zinedine Ferhat receive a second booking and receive his marching orders seconds before the referee blew his final whistle.
The DR Congo side now equaled Zamalek's Champions League record of five titles, three behind record champions Ahly – who last won the title in 2013.
Mazembe will now represent Africa in Japan's Club World Cup, where European champions Barcelona and Argentina's River Plate also compete, in December.
An uninspiring match saw Mazembe open the scoring in the 74th minute, when they were awarded a debatable penalty after Assale had been adjudged to have been fouled inside the area by the referee.
Samatta made no mistake from the spot to send the home fans into ecstasy, having extended their lead over their Algerian opponents to two goals with nearly 15 minutes left.
But after USM wasted a big chance to reduce the gap from point-blank range, it was their opponents who punished them on the break in stoppage time.
A through-on-goal Samatta turned this time from scorer to provider after setting up Assale with the second goal deep into injury time to make sure of victory for a fifth Champions League title.
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