The Dutchman was banned for six games after being sent off with a straight red card following a reckless foul on Manuel Schmiedebach in their 1-0 win over Hanover 96 on Saturday.
Schalke had appealed the initial decision.
"He must sit out four games of his (six-match) ban. The remaining two games are to be suspended until Jan 30 2016," the German football association (DFB) said.
"This means the forward will have to sit out these two games if he sees another red card until then."
Schalke, who face Real Madrid in the Champions League last 16 this month, are fourth in the Bundesliga after drawing 1-1 against Bayern on Tuesday.
Dutch international Huntelaar, 31, who has played in 17 of the 18 league games this season, has netted seven times.
(Reporting by Karolos Grohmann; editing by Sudipto Ganguly)
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