Chairman Eddie Mitchell confirmed the 21-year-old had been asked to stay away from Dean Court for a fortnight and invited to re-assess his career.
Stewart is understood to have been informed of the decision when he arrived for training on Friday, with Dan Thomas immediately recalled from a loan spell at Dorchester.
Thomas was on the bench for Cherries' League One clash with Southampton although the teenager missed yesterday's reserve team clash against Swindon with a strain.
It is believed boss Lee Bradbury's patience snapped when Stewart turned in late for training on Thursday. At one stage over the past two months, he failed to show at all for an afternoon weights session.
Stewart is also alleged to have been involved in two separate incidents when damage was sustained to hotel rooms during recent overnight stays while on duty with the club.
The Daily Echo has so far been unable to contact Stewart to discuss any of these allegations, although it is claimed he may have footed the bill for at least one of the incidents.
Signed by former Cherries boss Eddie Howe from Portsmouth in September, Stewart has been restricted to just four appearances for the club this season.
He was recently given permission to spend a week training with Premier League West Ham, having worked under current Hammers goalkeeping coach David Coles during his time at Pompey.
Stewart, who is just six months into a two-and-a-half year contract at Dean Court, was also a firm favourite of former Cherries assistant boss Jason Tindall, having played under him at Weymouth.
Mitchell told the Daily Echo: We have given Jon a couple of weeks to re-assess his career. We felt he hadn't been pulling his weight and felt it prudent not to have him around the squad for the next two weeks.
Personally, I am very sad about the situation. If I were in Jon's position, I would have trained as hard as I could, waited for my chance and proved my worth. I don't know his motives for not giving 100 per cent but that is the way we feel and that is the way we have acted.
His lack of enthusiasm and commitment in training caused us to have concern. He is due back in two weeks' time and there is going to be no give or take. He either works as hard as everybody else or he goes to play where he thinks he can fit in. We won't tolerate anything but 100 per cent. Any manager would have done the same as Lee and we are 100 per cent behind him.