His decision to step down came after he was criticised following Auxerre's home loss at the weekend after the 45-year-old Frenchman had spent a week away with Congo for friendly matches in the Middle East.
"I have made the decision in the interests of the club. It is regrettable given the relationship I have with the Congolese but the situation at Auxerre makes it necessary," he told the French sports daily L'Equipe.
Auxerre, who were relegated last season, are 12th in the standings with just four wins from 11 matches.
Wallemme took over as Congo coach in Aug. 2011 and added the Auxerre job in March but was unable to prevent the 1996 French champions from avoiding the drop.
Congo failed to qualify for next year's African Nations Cup under Wallemme but the side currently sit top of their 2014 World Cup second round qualifying group after two matches.