"The referee is a human being and is bound to make mistakes, but a lot of mistakes is questionable," Keshi told his post-match press conference at the Mane Garrincha National Stadium. "I'm not happy with the officiating."
Keshi was aggrieved that Emmanuel Emenike had a first-half goal ruled out for offside, although replays suggested the call was correct, and also felt France had been allowed to get away with over-zealous tackling.
Blaise Matuidi was only booked for an ugly challenge on Ogenyi Onazi that ended the Nigerian midfielder's game, while Olivier Giroud escaped punishment after appearing to catch John Mikel Obi with his elbow.
"If you look at the goal we scored, there was no infringement. On two occasions Onazi received very bad tackles and nothing was done about it. He is out now probably for weeks," Keshi added.
"This is the first time I've spoken about the referee in my life, because it wasn't good."
After a hard-fought game in Brasilia, France prevailed through a 79th-minute Paul Pogba header and an injury-time own goal by Joseph Yobo.
They will face either Germany or Algeria in the quarter-finals.
Pogba headed the ball into an empty net after Nigeria goalkeeper Vincent Enyeama failed to claim a Mathieu Valbuena corner and Keshi admitted that it had been a costly error by the usually dependable Lille player.
"It's only him that knows the reason he parried the ball rather than punched the ball," Keshi said.
"I was a long way away from where has. It was his decision. What happened, happened, and it cost us big."
France coach Didier Deschamps said that victory was his side's reward for not losing heart.
"The game lasts 90 minutes," said the former Marseille coach.
"Nigeria played the game we expected, with lots of physical intensity, and we had to respond to that. We can always start better, but we finished well."
France's victory continues a journey that began when they fought back to overturn a 2-0 first-leg deficit in their qualifying play-off with Ukraine in November.
Asked if France's qualification for the last eight meant that their tournament could already be considered a success, Deschamps replied: "At least it's not a failure.
"We had objectives, which went up after each match -- reach the last 16, finish top (of the group). Today it was to reach the quarter-finals.
"From what we've been through, to be here among the last eight shows something. But we won't get carried away.
"I'm very proud of the players. But the adversity will increase. It's another step and we'll do everything to climb that."
Deschamps was reluctant to be drawn into a debate about the referee.
"There are situations in a match where the referee makes decisions," he said.
"When they go against you, it's easier to talk about them. But you have to accept it. Could certain things have been sanctioned more firmly? It depends on what side of the fence you are."
Deschamps also praised goal-scorer Pogba, whose place in the team had come under threat from Moussa Sissoko after some mixed displays in the group phase.
"He's young, and criticism is part of the life of a top-level footballer," Deschamps said of the 21-year-old Juventus midfielder.
"It can be hard, it can be unjust, but it will toughen him up. Tonight he proved he has great, great potential by being a bit more straightforward in his play. I had no doubts about his capacity to be up to this level."