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.
"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.
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.
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."
