Striker Ahmed Raouf opened the scoring after 19 minutes when he headed home a pinpoint cross from lively right-back Ahmed Al-Muhammadi.
Mozambique defender Manu extended the gap two minutes before the break with another neat header.
Mpelempele pulled one back for the visitors six minutes after the restart with a fierce long-range drive.
However, Raouf scored his second of the night on 68 minutes after being set-up by Ahmed Al-Muhammadi once again to give ENPPI their first group-stage win
Diaa Al-Sayed enjoyed a winning debut after replacing Anwar Salama as ENPPI's head coach following the latter's resignation.
The petroleum club, who lost their first two games, moved up to third place in Group A with three points from as many games, three behind joint leaders ES Setif and Santos.