Thomson, 20, was fined and placed on the sex offenders register after pleading guilty to offences over the internet involving two girls.
"Hearts today announce that Craig Thomson is suspended with immediate effect," the club said in a statement on their website.
"No further comment will be made by the club."
The club had come under pressure to sack or suspend Thomson, who is a Scotland Under-21 international, but had announced on Monday they were standing by the player.
Children's charity Children 1st and the club's water sponsor were among those urging the club to take action.
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