The American midfielder is continuing his comeback from a long-term injury and Dougie Freedman confirms he wants to keep the 27-year-old at the Reebok Stadium long-term
The American joins Seyi Olofinjana at Hillsborough, after the Nigerian moved on a similar deal from Hull City on Wednesday.
Holden's contract expires at the end of the season and, despite fitness concerns in recent years, Trotters boss Dougie Freedman is keen to keep the 27-year-old long-term.
"This is the best move for Stuart," Freedman told reporters. "We had a good chat and I informed him that we want him with us next season."
Holden has appeared in just three games for Bolton since making his comeback following a near 16-month spell on the sidelines as he recovered from a knee injury suffered in March 2011 and the ensuing complications.
Wednesday boss Dave Jones told BBC Radio Sheffield: "He just wants to get going again, that is the most important thing to him.
"He's quality on the ball, he's got an eye for a goal and if hadn't had the injuries he's had then we wouldn't have been able to get him."