Enyimba are the only NPFL side that progressed to the CAF Confederation Cup group stage.
Enyimba are the only NPFL side in the CAF competitions and had their NPFL game against Akwa United postponed.
Isiaka Oladuntoye gave the People's Elephants the lead in the 48th minute.
Stanley Dimgba made it two when he converted a penalty in the 81st minute.
The victory gives Enyimba all three points going into their next fixture away against Club Athletique.
Enyimba are Nigeria's most successful club side on the continent after a consecutive triumph in the CAF Champions League in 2003 and 2004 and aim to be the first NPFL side since Dolphins FC in 2005 to get to the final.
The Aba based side were drawn alongside Willamsville of Ivory Coast, Club Athletique of Congo and Malian side Djoliba who knocked out MFM.
Away vs Club Athletique Tuesday, May 15
At home vs Williamsville Tuesday, July 17
Away vs Williamsville Friday, July 17
Away vs Djoliba Friday, August 17
At home vs Club Athletique, Tuesday, August 28.