Babeker sealed victory with a superb volley ten minutes from time and give Merreikh a first leg cushioning in the semi-final, ahead of the return leg next week in the DR Congo city of Lubumbashi.
It was the seventh goal for the forward, currently the leading marksman in the premier continental club championship.
Midway into the second half, substitute Thomas Ulimwengu drew level for the four-time winners, cancelling Francis Coffie’s first half lead.
The game that pitted Merreik coach, Diego Garzitto against his former club, Mazembe, a side he guided to win the ultimate in 2009, saw the hosts getting off to a blistering start that unsettled the Congolese.
Chances upon chances began to pour in for Merreikh, who survived an early scare after goalkeeper Jamal Salim’s shot from a goal-kick bounced off the head of Mbwana Samata but the crossbar was to his rescue.
Babeker and Ivorian-import Didier Lebri were the worst offenders failing to make the most of the opportunities that came their way after taking control of the game. On 11 minutes, Lebri headed wide from a Babeker cross, before Solomon Jabason blasted wide from a Lebri assist on the half-hour mark.
The home fans had to wait for 41 minutes before they could finally smile after a Jabason thunderbolt was spilled by Mazembe goalie Muteba Kidiaba, and Coffie, who was lurking around tapped home for the opener.
The tempo of the game died in the second half with Mazembe beginning to make inroads largely thanks to a double substitution that saw Daniel Nii Adjei and Jean Kasusula make way for Nathan Sinkala and Merveille Bope.
On 65 minutes, Roger Assale broke off on the counter only to be denied by Salim who saved his goal bound shot with his foot.
Twelve minutes, Assale set up Ulimwengu who shot past Salim for the equalizer to silence the home crowd.
On 80 minutes, Babeker brought the stadium back to its feet, controlling a cross from captain Abdalla Ragei on his chest before volleying past a hapless Kidiaba to secure victory.
The second leg will take place on Sunday, 4 October 2015 in Lubumbashi with the winner facing either El Hilal (Sudan) or USM Alger in the final.