His opposite number, Zambia goalkeeper Kennedy Mweene, saved a point for the champions by converting the 85th minute spot- kick to force a 1-1 draw in Group C.
Television replays certainly suggested that if Nigerian defender Ogenyi Onazi touched Zambia's Emmanuel Mayaka as he fell, it was unintentional and could well have been outside the penalty area.
"It was the worst decision I have seen live. I don't know what is happening with the officiating," Enyeama fumed.
We had a terrible official in the first game too. But a decision like the one today does not belong in African football, and certainly not in a match of the magnitude of the champions against Nigeria," Enyeama fumed.
"I am really mad about it."
The penalty was the second in the Group C game, the first real clash of the heavyweights in the tournament.
The first was awarded to Nigeria after 25 minutes when Zambian defender Davies Nkausu brought down Ahmed Musa.
Nigerian midfielder John Obi Mikel, who has scored two FA Cup goals but none in 261 Premier League appearances for club side Chelsea, took a weak penalty, firing against Mweene's post.
Although the referee awarded Nigeria a corner thinking that Mweene had saved the kick, the goalkeeper said afterwards, "No, I never got a hand to it. It hit the post."
The penalty was the fourth Zambia have conceded in their last four successive matches in the tournanent - and all four have been missed.
They conceded one in last year's semi-final against Ghana, which Asamoah Gyan missed and final against Ivory Coast, which Didier Drogba missed, forcing the final to a penalty shootout which Zambia won.
The third miss came on Monday when Saladin Seid of Ethiopia saw his penalty saved by Mweene at the same end of the Mbombela Stadium.
Nigeria eventually went ahead when Emmanuel Emenike beat Mweene with a low shot after 57 minutes.
Mweene kept his cool when his chance came to equalise, sweeping the ball high into the roof of Enyeama's net.
"For a goalkeeper to save a penalty it is hard, but to take a penalty, it's even more difficult," man-of-the-match Mweene said.
"You have to walk from one end of the pitch to the other. It's difficult, but I kept my cool and scored."
Zambia and Nigeria have two points from two matches, with Ethiopia playing Burkina Faso in the later game.