The Peace Boys started the game on the front foot but their impressive showings yielded no tangible result as both sides went into the break goalless.
After the interval, King Osanga shot the home side ahead in the 49th minute.
El Kanemi players, spurred by the Peace Boys' opener, fought back and carved out two goals within five minutes through Kingsley Maduforo and Nuru Mohammed in the 65th and 70th minutes.
Kennedy Boboye's men threw everything into attack with an aim to rescue the tie but the Borno Army held on to claim victory.
El Kanemi will return to Maiduguri on Tuesday ahead of their participation in a pre-season tournament holding in Kano from December 1.