The medal, one of four golds that Owens won at the Berlin Games in front of Adolf Hitler, is "a part of world heritage," Bach said Wednesday.
"(It has) an importance far beyond the sporting achievements of Jesse Owens, which is part of world history," the IOC president said in an interview with The Associated Press at an anti-doping conference in South Africa. "To put this up for an auction is for me a very difficult decision (to accept)."
The International Olympic Committee will not intervene in the sale. SCP Auctions says the medal could go for more than $1 million when the auction opens later this month.
"Whether this medal is purchased by a private individual or an institution, SCP Auctions and our consignor share in the feeling that the ideal place for Jesse Owens' gold medal is on display in a museum where it can be shared with the public and perpetuate Owens' inspiring legacy," said Dan Imler, vice-president of SCP Auctions in Laguna Niguel, California.
According to the auction house, Owens gave the medal to his friend, movie star Bill "Bojangles" Robinson, to thank him for helping the athlete find work in the entertainment industry after he returned from Germany. It is being sold by the estate of Robinson's late widow.
SCP Auctions confirmed that the medal is genuine. The whereabouts of the other three original gold medals is unknown.
Owens was given a replacement set of medals, which now form part of an exhibition at Ohio State University, the school he attended.
Owens won gold in the 100 metres, 200 metres, 4x100 relay and long jump, a defining moment in Olympic history. He died in 1980.