Jordan, then with the Chicago Bulls, scored 38 points in Game 5 of the 1997 NBA Finals against the Utah Jazz despite suffering from flu-like symptoms. Jordan gave the shoes, autographed, to Utah Jazz ball boy Preston Truman.
Truman offered the shoes for auction through Grey Flannel, which included the items in a 900-lot sports memorabilia auction Wednesday.
The auction house said the highest offer, from an unidentified bidder, for Jordan's shoes was a record-setting $104,765. The previous high bid for game-used sports shoes was about $31,000 last month for a pair of shoes Jordan wore as an NBA rookie.
Also in Wednesday's bidding, Grey Flannel said the uniform and cleats worn by quarterback Brett Favre when he broke the NFL's all-time touchdown record drew a high bid of $29,544 and the World Championship ring given to outfielder Sam Byrd for the New York Yankees winning the 1932 World Series went for $65,048.