Yakubu Aiyegbeni, after fluffing several early chances, netted in the 42nd minute to give the World Cup-bound Nigeria a much-needed win after they had lost their opening game to Egypt.
The penalty was awarded after a handball by defender Romuald Boco, who stopped a header on goal by Peter Odemwingie.
Benin twice hit the woodwork with blistering shots from Stephane Sessegnon in the first half and Nouhoum Kobena after the break and kept Nigeria on the back foot for much of the game.
"We expected a tough game but this has helped to build our confidence," Nigeria coach Shaibu Amodu told reporters.
"The good side is that we showed our experience. We had to be cautious and guard against any mistakes because they were capable of punishing us."
Benin might have had an early break when Nigeria captain Joseph Yobo's slip gifted Razak Omotoyossi a chance to score but the Everton centre back recovered quickly to force a corner.
Aiyegbeni missed a simple tap-in in the 15th minute when he was set free on goal by a clever through ball from Kalu Uche but hit the ball wide.
He had another opportunity just before the half hour but failed to react quickest to a rebound in the Benin box.
Benin's inspirational midfielder Sessegnon hit a powerful shot on to the crossbar in the 39th minute after a probing run at the Nigeria defence.
With three Nigerian-born players in their team, Benin proved a gritty outfit and also set up several second half chances.
The closest fell to Kobena who hit the crossbar from a tight angle.
Sessegnon almost went narrowly wide with a driving shot and the persistent running at the Nigeria defence by Mouri Ogunbiyi kept Benin in the game until the late.
But Boco's trailing hand ruined all their hard work as the referee had no choice but to award Nigeria the penalty.
Benin's coach Michel Dussuyer said a win over Nigeria would have been a dream before adding: "The difference between the dream and reality for us was the crossbar."
The result left Benin facing elimination as they have just one point from two matches. They will be up against champions Egypt next week.
