It is the second coaching change in six months for the Pretoria club, owned by the family of Confederation of African Football president Patrice Motsepe.
Cardoso is a former coach at Rio Ave in Portugal, Nantes in France, LaLiga outfit Celta Vigo and AEK Athens.
Last season he took the Tunisian club Esperance to the African Champions League final but was fired in October after a poor start to the new season.
Mngqithi’s departure follows Sundowns drawing their opening two matches of the group phase of this season’s Champions League and a shock loss in last month’s South African League Cup final.
He had taken over in July from Rulani Mokwena, who was sacked despite winning the league by a record 23-point margin.
At the Club World Cup next June, Sundowns are in Group F with Borussia Dortmund, Fluminense and South Korean club Ulsan HD.