Former Paris St Germain defender Fournier had been in charge of the team since last June
"The Auxerre board gathered today and appointed Jean-Guy Wallemme as the new coach", the club said in a short statement on their website (www.aja.fr).
The club did not provide any contract details and it was not clear if Wallemme would remain as national coach for Congo, who have a World Cup qualifier in Burkina Faso scheduled for June 1.
Wallemme, a former Saint-Etienne and Lens coach, has been in charge of Congo since August.
Auxerre lost 2-0 at home to Evian on Saturday to stay 19th in the 20-team table on 24 points from 28 games.