Magilton had complained to referee Mike Jones about the use of the multi ball system and was ordered from the dug-out.
He was given a suspended ban as explained by Club secretary Sally Webb explains.
"We had a very fair hearing, the suspension on the touchline ban means that it will come into place if Jim faces another charge next season. If he goes through the year with no disciplinary action then the ban will be wiped off in May 2009."
"Jim was very upset at the multi-ball system at Stoke and doesn't like the system in general, we will be asking the clubs at the Football League AGM to vote on scrapping the system."