The American midfielder is continuing his comeback from a long-term injury and will play with the struggling League Championship side until April 24.
Bolton loaned the American midfielder to Sheffield Wednesday until April 24 on Thursday, providing him with the opportunity to receive more playing time as the 2012-13 campaign winds down.
Instead of helping Bolton try to seal a place in the Championship promotion playoff over the next month, he'll attempt to keep Sheffield Wednesday in the second-tier league, with the club hovering over the relegation zone, a point clear of safety.
Holden's contract with Bolton expires at the end of the season, but manager Dougie Freedman ensured that the club intends to bring him back with a new deal in comments made on the club's official Twitter account.
"This is the best move for Stuart," Freedman said. "We had a good chat and I informed him that we want him with us next season."
Holden has appeared in three games (one league, two FA Cup) for Bolton since making his comeback following a nearly 16-month spell on the sidelines as he recovered from a knee injury suffered in March 2011 and the ensuing complications.
Seven of Sheffield Wednesday's nine games remaining in the season take place during Holden's loan spell, and he'll return to Bolton with the Trotters having two games to play, with potentially a few more should they reach the promotion playoffs.