Pinnick, who was present at the match venue, told journalists after the game that he has taken up the issue with the appropriate body following the manner Algerian referee Mustapha Ghorbal handled the game.
He also said that the Nigerian side did not deserve to win in Cotonou.
The NFF boss said: “The officiating was very poor and I have notified the authorities concerning it.
“I wasn’t really impressed with our players. I don’t know what happened. They are all very highly rated players, some of the best in our league but to me they didn’t live up to expectations.
“Some of those factors like the officiating must have affected them. But like I said, we will do everything possible in the second leg to make sure we qualify for CHAN.
“I believe we will do our best on the second leg in Kano.
“But I can say emphatically that the officiating was very poor and the turf too affected our game but we will be able to overcome those two challenges in the next game and qualify. By God’s grace we are going to work hard to make sure we qualify.”
It could be recalled that Benin Republic team was awarded an 89th minute penalty converted by their skipper Seibou Mama following a foul on a Beninoise player inside the box by Azeez Aremu.