The German football legend also sought to hide the sum from tax authorities, the magazine said, in the latest embarrassment for Beckenbauer, who is being investigated by Swiss authorities in relation to corruption allegations over the awarding of the 2006 World Cup to Germany.
The latest revelation drew anger from German Football Federation chief Reinhard Grindel, who accused the man nicknamed "the Kaiser", 71, of lying and misleading the public.
According to Spiegel, the sum was taken from a donation of €12 million made by a World Cup sponsor - the gambling company Oddset.
"We know that Franz Beckenbauer worked for Oddset in the framework of the World Cup. But we were not aware that he drew a sum of €5.5 million ($6.2 million) from the budget of the organisation of World Cup 2006," Grindel said in a statement.
"Obviously, given these conditions, we cannot say that he had worked on an unpaid basis for the organising committee," the DFB boss added in a statement from Athens, where he was attending the UEFA congress.
Beckenbauer did not declare the sum to tax authorities for four years, according to Spiegel.
But following checks by tax authorities, the DFB was ordered to pay a million euros in withholding taxes on the sum in 2010. Beckenbauer subsequently repaid those taxes levied to the DFB.
Beckenbauer captained Germany to the 1974 World Cup and coached the side that won the trophy in Italy in 1990.
But his reputation has been badly tarnished by his role in the ongoing scandal over the awarding of the 2006 World Cup finals to Germany.
Swiss authorities are investigating him, along with three other members of the organizing committee over "allegations of fraud, criminal mismanagement, money laundering and misappropriation."
The probe came after a Spiegel report last October that a secret fund of 10 million Swiss francs (€6.7 million) was used to buy the hosting rights of the 2006 World Cup.
The money allegedly came from the late Robert Louis-Dreyfus, ex-boss of Adidas, at Beckenbauer's request, and was handed over in 2000, just before Germany were awarded the 2006 finals by a narrow vote.
In May, an independent inquiry commissioned by the DFB said it could not rule out that Germany bought votes to secure the 2006 World Cup.
Beckenbauer has always denied any wrongdoing.