The club's five-strong ethics committee, in a statement late Tuesday, accused Tönnies of having "violated the ban on discrimination contained in the club's statutes" after a lengthy meeting in which Toennies had to explain himself.
But the body dismissed the accusation of racism as "unfounded" and consequently spared him the heavier sanction of dismissing him.
The 63-year-old has been sharply criticized for saying more power stations should be built in Africa, "then Africans would stop felling trees and producing children when it gets dark".
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The billionaire businessman, who employs 16,500 people and has assets estimated by Forbes at around €2.2 billion, made the remark at a forum in Paderborn last Thursday while criticizing tax increases to fight climate change.
On social media, numerous Schalke fans and former players demanded his resignation as chairman of the club's supervisory board, while senior figures in German football and politics have condemned his comment.
Politician Dagmar Freitag, the chairman of the sports committee in Germany's parliament, the Bundestag, slammed the finding of Schalke's ethics committee.
"If I had pigeonholed an entire continent and its population, then it would be racism rather than 'just' discrimination, as far as I am concerned," she told broadcaster NRD.
"Such lapses are a break in what is taboo, without scruples, and their effect on society is – especially in these times – devastating."
Tönnies had apologized for his "inappropriate" words on Sunday, insisting he backs Schalke's values against "racism, discrimination and exclusion".
Justice Minister Christine Lambrecht had previously called on the German Football Association (DFB) to "deal" with Tönnies.
"Racism must be loudly and clearly contradicted" at every opportunity," the politician told the Funke media group.
"Nowhere is integration as successful and quick to work as in sport – that must not be put at risk."
Cacau, the Brazil-born former Germany star who heads the DFB's integration committee, was also stunned by Toennies comment.
"The longer I think about it, the more unimaginable it becomes that a man of his position and experience speaks so... disparagingly about the population of an entire continent," said the 38-year-old.
Former Schalke forward Gerald Asamoah, Germany's first black international, said he was left "somewhat speechless" by Tönnies remark.
"I have been working with Clemens Tönnies for a long time, and we have been close friends for a long time," wrote the 40-year-old Asamoah on Instagram.
"He never behaved in a racist manner towards me.
"I was very surprised, shocked and injured by his statement."
The comments are a distraction for North Rhine-Westphalia's Schalke, under new head coach David Wagner, who start their league season at Borussia Mönchengladbach on August 17th.
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