The American was forced to watch from the stands as the Owls earned a 1-1 draw against Ipswich Town at Hillsborough on Saturday after picking up a knock during their stalemate at Blackpool during the week.
Holden joined from Bolton Wanderers on a one-month emergency loan in March, and Jones appreciates his contribution.
"Bolton will pull Holden back so we couldn't risk him today considering the favour we've had from them," said Jones. "We thank Stuart Holden for his time here."
Holden appeared four times for Wednesday.