The Frenchman leaves with the team lying second in their group and still able to qualify for next year's tournament if they beat group leaders Senegal on Saturday and finish with a home win against Cameroon next month.
"I asked to have my contract terminated after a year in the job. I did not have the best conditions to work in or the right philosophy around my team and prefer to leave," Nouzaret told Kinshasa's Radio Okapi.
"I think everything will go fine in those last two qualifiers. But the problem in Congo is not the national team but officials who do not create the conditions to build the side.
"It needs to be a mix of locally-based and professional players from European clubs and I've always said we need to create a unity among them. The team is also missing an iconic player of the calibre of [Didier] Drogba for the Ivory Coast and [Samuel] Eto'o in Cameroon."
Nouzaret was in charge of 13 games over the last year, winning six, drawing one and losing six.
The 67-year-old coach has extensive coaching experience in France's Ligue 1 and had two spells in charge of Ivory Coast and one at the helm of Guinea's national team.
Assistant coach Otis Ngoma replaces him for Saturday's match in Dakar.
