Jemaa, an injury doubt before the tournament, won it on the stroke of full-time after cutting inside two defenders to power the ball home from close range.
It gave Tunisia a second Group C win after their 2-1 success over Morocco.
Debutants Niger, who showed a marked improvement from the side overwhelmed 2-0 by co-hosts Gabon in their first game on Monday, look virtually certain to exit the tournament.
The first two goals came in the opening seven minutes but chances flowed freely thereafter.
The opener was a sublime move and finish, the second bordered on the bizarre.
Tunisia's left winger Youssef Msakni dribbled past four defenders before placing the ball past goalkeeper Daouda Kassaly after four minutes.
Niger were soon level when a long clearance into the Tunisia penalty area dropped with awkward back spin, fooling goalkeeper Aymen Mathlouthi who was distracted by an attempt from Moussa Maazou to slap the ball which bounced on to the head of William Tonji Ngounou and into an empty net.
"It was important for us to our first goal of the tournament," said the journeyman striker who plays in the Swedish third division.
Msakni missed two chances and at the other end Maazou wrought havoc in the Tunisia defence with his burly frame. His power and pace twice took him past the defence but he shot agonisingly wide.
Both sides hit the woodwork before Jemaa's goal. Tunisia might have made it 3-1 deep into stoppage-time when Oussama Darragi hit the underside of the bar but the ball bounced back into play.
"It was a hard game, they really made us struggle in the first half. But we got better in the second half," said Tunisia captain Karim Haggui.
Gabon dramatically beat Morocco 3-2 later on Friday in Libreville, ensuring Tunisia's progression to the quarter-finals.
