Chijoke Akuneto and Monsuru Bashiru scored both goals for MFM, while Amachi was on target for the visitors.
MFM created the first real chance of the game with Bashirua��s attempted lob in the fifth minute going inches wide.
The hosts came close again two minutes later through the lively Akuneto.
The forward turned inside the box following a beautiful pass by Chukwuka Onuwa but his effort was saved by MC Algera��s goalkeeper Chaal.
It was the turn of the visitors to test MFM goalkeeper Ospino Egbe three minutes later and he did well to palm away Amadaa��s fierce shot from the edge of the area.
With the away side putting up stiff resistance at the rear MFM struggled to create clearcut chances afterwards.
Play was stopped in the 20th minute after Bashiru Monsuru appeared to have slumped but he was deemed okay to continue with the game after he was attended to by a combined team of MFM and MC Alger medics.
MFM made the first substitution of the game in the 23rd minute with Ubakanma Peter coming in for Okorom Stanley.
Akinyemi Nojeem tested Chaal in the 27th minute but the latter did well to push his shot into touch for a corner kick.
The home team made the breakthrough nine minutes before the break when Akuneto converted from the spot after he was tripped inside the box.
The visitors nearly equalised before the break but Egbe prevented Balegh effort from going into the net.
Akuneto missed a glorious chance to double his sidea��s lead two minutes after the break after he was set up by teenager Lawal Abayom but his goal-bound shot was saved by Chaal.
MC Alger equalised in the 55th minute through Amachi who fired past the on rushing Egbe.
The hosts took control of the game afterwards but were unable to find a way past the MFM defence.
Monsuru scored the winner five minutes from time with his surprise shot from outside the box sailing into the net.