A former England Under-21 international, Stuart tested positive for cocaine and marijuana when the FA's doping control unit visited Charlton's training ground on 17 November.
The 21-year-old was charged with misconduct by the FA, and was sacked by his club after becoming the fourth Charlton player to fail a drugs test in the past three years.
Stuart had claimed that the cocaine was contained in a cigarette without his knowledge, and that he had smoked it on a Thursday night four days before the random drugs test. But the Commission heard evidence that it was highly unlikely that the drug had been taken that way, or at that time.
Steve Double, a spokesman for the FA, said: "The Commission heard Stuart had been involved in a traumatic family crisis at the time of the incident and decided he should be subject to three months' counselling and rehabilitation, during which time his suspension from football will continue. He will appear before the Commission again in three months' time for the reports to be assessed. Sentencing will be deferred until that date."
After the hearing Brendan Batson, the Professional Footballers' Association deputy chief executive, criticised Charlton's decision to terminate Stuart's contract so quickly - against the players' union's advice. "I think they've acted very prematurely, bearing in mind what's gone on today," Batson said. "I would hope that they may reconsider their position and give him as much support as possible. Everybody makes mistakes."
Tottenham have agreed to pay for the medical examination which the Everton defender Andy Hinchcliffe failed earlier this month when his proposed move to Spurs fell through - after the bill was mistakenly sent to the England international.
Hinchcliffe received the pounds 500 bill at his home. Everton's manager, Howard Kendall, said: "I'd like to think that this is surely some kind of error. We are treating the whole thing as a bit of joke and returning the bill to Tottenham."Reuse content