But Congo took just four minutes to respond, Tresor Mputu finishing superbly from Dieudonne Mbokani's cross.
CNN: Keita goal helps Mali grab first win of Africa Cup of Nations
In 2007 Mputu was top scorer in both the Champions League and Confederation Cup.
"I promised the team that I wouldn't leave before winning a cup, and now I've managed to do this, " Mputu said.
The victory may signal the departure from Mazembe of the highly-rated Mputu Mabi, as the 24-year-old admitted after the historic win.
They will parade their star striker Mputu Mabi, who was the player of the tournament when DR Congo won the African Nations Championship (CHAN) earlier this year.
Yet without Mputu, the team has made it to the Club World Cup final, beating Mexico's Pachuca and Brazil's Internacional along the way, without conceding a goal.
That gave the DR Congo side the win, despite being hampered by the absence of two key players - top scorer and captain Tresor Mputu Mabi and midfielder Guy Lusadisu.
Club president and sponsor Moise Katumbi, the governor of Katanga province, had made it clear that he would be happy for Mputu to leave if the team became African champions.
At a goodwill tournament in Rwanda earlier this year, Mputu -- considered to be the best footballer still playing on the continent -- was banned by FIFA for a year after karate-kicking a referee.
"There was many times my life was at risk ... but with the end of the war I am happy that there is now peace, " TP Mazembe's captain Tresor Mputu told CNN last year before his debut in the competition.
The closest the hosts came to breaking the deadlock came at the end of the first leg as Tresor Mputu Mabi, who scored the crucial away goal for Mazembe in Nigeria last weekend, found Kalauyituka Dioko, but his header was saved by Augustine Brown.
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