The result condemned the three–times champions to finishing second and a probable encounter with the Black Stars of Ghana in the Round of 16.
The then group leaders started on the wrong footing as Leon Balogun failed to deal with a routine back pass.
It led to the ball being snatched by Lalaina Nomenjanahary to score the first goal for the competition debutants after only 13 minutes.
The Eagles, who won each of their two previous matches by the odd goal, then showed a palpable lack of mental power to respond.
Samuel Kalu fluffed a great pass by Ahmed Musa in the 19th minute.
Musa himself, left with the goalkeeper to beat as a pass found him in the penalty box, bungled with a poor first touch.
His subsequent attempt to dribble the goalkeeper failed.
In the second half, instead of working hard to get on level terms in no time, Nigeria quickly found themselves further behind.
That was when substitute Wilfred Ndidi deflected a free-kick by Carolus Andrea past a wrong-footed goalkeeper Ikechukwu Ezenwa.
A deep soul–searching is now imminent in the Nigeria camp after such a flat performance.
They lost to a team rated lower than 100th in the world and we’re making their first-ever appearance at the Africa Cup of Nations.
First touches left the Eagles’ midfielders and forwards down, as they made heavy weather of simple passes and controls.
Also, creativity was totally lacking in a team that earned a ticket to Egypt with a match to spare.
Skipper Mikel Obi, making his 89th appearance for the Eagles, was a shadow of himself, while Alex Iwobi was no magnificent difference when he came on.
Moses Simon and Wilfred Ndidi brought no spark or innovation on board when they were introduced.
Such a sound beating by a team that had never scored against Nigeria in four pervious meetings was a dampener.
It will now be interesting to see how the Eagles overcome this adversity and put up a show in their Round of 16 encounter at the same venue on Saturday.
Madagascar finished the group stage unbeaten and scored two lovely goals from dead-ball situations.
The Super Eagles have however not been able to make hay from free-kicks in recent memory.
This calls to question the continued delegation of the responsibility to one man who has refused to perfect his act.
Three opportunities presented themselves from 20 yards and they were all wasted in non-challant manner.
Coach Gernot Rohr, who rang five changes to the team which defeated Guinea on Wednesday, must now come up with a solution.
He must bring up the formula to lift a dispirited dressing room before Saturday.(NAN)