Madine, 22, is due to attend Leeds Crown Court on September 2 after being charged with assaulting a man in a Sheffield city centre nightclub in February 2012.
The Gateshead-born forward stepped off the bench in the Owls' first two games of the season, but was omitted from the squad selected for the weekend defeat to Burnley.
"The club has taken a decision on Gary Madine to allow him to concentrate fully on his court case, which he has coming up in two weeks' time," Jones told reporters after Saturday's 2-1 loss.
"The club has made that decision and I cannot say too much about it. It's another player that we lose but it's Gary's future and it's more important than football.
"He needs to be fully focussed on that and that is what the club has decided. I have been there myself, I know what it takes and it's a big thing for him," added Jones, who was cleared of child abuse allegations in 2000.
"He needs to make sure that he is aware of what he has got to do. It's a big call by the club and people will ask if it's the right call but it is the lad's future."
Jones also denied Madine could soon leave the club following summer speculation over his future.
"Rumours about him being lined up for a move are not true because I think it will be difficult for him to move away if he's in court in two weeks' time," Jones said.
"He has still got to train with us because he will be two weeks preparing for court and two weeks in court and we won't see him for those two weeks."