They scored a second in injury time through Joseph Yobo's own goal that has set up a tie against either Germany or Algeria in the last eight.
Here, Sports Mole takes a closer look at the events that unfolded at the Estadio Nacional.
On Target 5
On Target 2
Was the result fair?
On the balance of play, France just about deserved to win the match. It was an even affair, especially in an entertaining first half, where both teams saw an equal amount of the ball yet failed to create any real chances. After the break, each side were guilty of squandering possession cheaply, while there were also a number of mistimed challenges. However, as the game entered the final 20 minutes, France started to take control and it only looked like a matter of time until they would break the deadlock. Indeed, they made their pressure count when Pogba headed in and saw out the rest of the match to book a place in the last eight.
Although it was not a free-flowing display of attacking football that France have shown in the early stages of the tournament, they produced moments of brilliance that ended up deciding the contest. Raphael Varane was impressive in the heart of the defence throughout the match and his partnership with Laurent Koscielny kept the Nigerian attack at bay. The midfield was a crucial area in the match and eventually Pogba and Yohan Cabaye were able to dominate as the game entered the closing stages.
However, it was only after Antoine Griezmann came on that France began to look like winning the match. He almost made an immediate impact when his precise pass sent Karim Benzema through on goal, with the striker seeing his effort cleared off the line. His entrance seemed to energise his teammates and they were able to find an extra gear to go on and claim the win.
Nigeria started the game brightly and it looked like their forwards were going to give France a lot of problems. However, they rarely got in behind and only two of their shots on goal were on target. What will have been even more frustrating for manager Stephen Keshi is that they won a number of corners and set pieces in dangerous situations, but each time their delivery into the box was poor.
Nigeria more than held their own, but after an hour their players started to tire and they badly missed midfielder Ogenyi Onazi, who had to leave the pitch injured. They finally conceded with 11 minutes to play after a period of French pressure, but keeper Vincent Enyeama will feel that he could have done better. He failed to clear Valbuena's corner at the near post allowing Pogba a simple header. It was a disappointing end to the tournament for Nigeria, but there are plenty of positives for this young side to take going forward.
Sports Mole's man of the match
Mathieu Valbuena: The 29-year-old was a crucial part of his team's victory today. He set up the first goal when his corner was headed in by Pogba, before he saw a cross diverted into his own net by Yobo to seal the win late on. He was at the heart of everything good all afternoon and with his future at Marseille looking uncertain, there are plenty of clubs who will be interested in signing him based on this impressive showing.
Enyeama was proving to be a nuisance for France after producing outstanding saves to deny Pogba and Benzema, but his mistake proved costly for his side. He badly misjudged Valbuena's corner that ended up being headed in at the back post by Pogba and his team were unable recover from the setback.
A number of refereeing decisions have been talking points of the knockout stages, but thankfully Mark Geiger was not forced into making any controversial calls. He correctly disallowed a strike from Emmanuel Emenike in the first half for an offside decision and handed out just one booking to Blaise Matuidi. In a scrappy match the American referee managed the game well and will surely be a candidate to officiate at the latter stages of the tournament.
France: France will take on the winners of Germany and Algeria's last-16 tie that is being played later this evening.
Nigeria: The Super Eagles will begin their Africa Cup of Nations qualifying campaign in September.