Despite the result, the Congolese club remain bottom of the group, but they are now just three points behind top side Cotonsport of Cameroon, with all to play for in the final two games in the pool.
It was a weakened Enyimba side that took to the pitch and they were behind on 18 minutes when Nvete Luyeye scored for the home side.
Mputu Mabi doubled the advantage midway through the second half from the penalty spot after an Enyimba defender had handled the ball, and Patou Kabangu rifled home a third 10 minutes from time to seal the points.
With all teams having played four matches, Cotonsport head the group on seven points, followed by Enyimba (six), Al-Hilal (five) and TP Mazembe (four).
On Saturday, Cotonsport beat visiting Al-Hilal as Baba Ousmaila got the only goal of the game. Hilal had Alaeldin Gibril sent off midway through the second half.