The club yesterday announced they were standing by the player, following a conviction for "lewd, libidinous and indecent behaviour".
However, a short statement on the club's official website, www.heartsfc.co.uk, this morning read: "Hearts today announce that Craig Thomson is suspended with immediate effect. No further comment will be made by the club."
The 20-year-old full-back earlier this month pleaded guilty, was fined and placed on the sex offenders register in relation to his inappropriate conduct towards two underage girls over the internet.
And yesterday one of the club's sponsors - MacB Water - announced they were withdrawing support as official water sponsor of the Jambos, a deal worth more than 5,000.
A MacB spokeswoman said: "As a company with strong family values, we are left with no choice but to terminate our relationship with the Hearts Football Club.
"Along with countless others, fans and co-sponsors alike, we are extremely disappointed with the club's handling of this situation and as a result can no longer continue our support."
Hearts manager Jim Jefferies admitted yesterday, before the club's U-turn: "There will be some games now where this gives us a situation.
"We have to make sure that if Craig ever gets back in the team - and let's not forget there's competition for places - how will he handle what's coming to him?
"We have to be sure as well because at the end of the day that's going to affect the performance of the rest of the players if it becomes a bit of a sideshow which gets out of hand."
Meanwhile Hearts are set to escape punishment for the fan assault on Neil Lennon which took place at their match against Celtic at Tynecastle on May 11.
The Scottish Premier League are expected to conclude that neither club had a case to answer in respect of their responsibilities.
However, the SPL has raised serious concerns about inconsistency of policing at football grounds.
The SPL's match delegate, Willie McDougall – formerly head of security at the Scottish Football Association – described the atmosphere on May 11 as one of the worst he had encountered at any football match, although only two fans were arrested.
One of those was the spectator who was able to make his way from his seat in the main stand and reach the Celtic technical area unhindered.
Hearts had arranged a meeting with Lothians and Borders Police prior to the game specifically because they had been concerned about the atmosphere when the teams met at a previous encounter at Tynecastle, on November 10 last year.