Thomas has won 100 caps for Wales and toured with the Lions in 2005
Castleford have been fined £40,000 by the Rugby Football League after fans aimed homophobic abuse at Crusaders winger Gareth Thomas.
Thomas, 35, announced in December 2009 that he was gay.
"The RFL finds homosexual abuse unacceptable, which is reflected in the size of the fine," RFL spokesman John Ledger told BBC Sport.
Castleford chief executive Richard Wright said he was "shocked" by the decision, adding the club will appeal.
"The evidence does not support the decision and does not in any way support the scale of the penalty. We totally refute the outcome of the hearing," stated Wright, whose club have had half the fine suspended until the end of 2011.
The Tigers were found guilty of unacceptable behaviour, of breaching the RFL's Respect Policy, of misconduct by their supporters and of conduct prejudicial to the interests of the sport.
The tribunal which looked into the incident criticised the club for perceived failures in trying to stop the chanting and in identifying the perpetrators, as well as for failing to conduct a "meaningful inquiry" afterwards.
Thomas, who captained Wales and the British and Irish Lions in rugby union before switching codes, was subjected to the abuse during the Crusaders' visit to The Jungle in the Super League on 26 March.
Castleford's legal advisor, Rod Findlay added: "The club condemns any person who makes or chants obscene remarks towards players or officials.
"But the charges against the club are not that there was chanting, they are that the club failed to take its best endeavours to prevent or stop any chanting.
"This the club refutes totally. The club has a well-established system for dealing with chanting and could not have done any more on the day."
Thomas's manager Emanuele Palladino issued a statement congratulating the RFL on its action.
"This has been an historic day," he said. "Gareth Thomas is all about delivering positive messages and positive changes and, to that end, this was a huge step forward for Gareth and the world of sport.
"It is not about the fine, but rather recognition that this behaviour from a small section of the Castleford fans is not acceptable in 2010.
Our sport is viewed by Stonewall as a model with the way it deals with issues around homosexuality
RFL spokesman John Ledger
"Unfortunately, what happened at Castleford could not be ignored. We are delighted that the RFL has taken action against what is a serious and upsetting incident for all parties.
"Its stance makes it clear that behaviour like this is not, and should not be acceptable in the world we live in today."
Castleford will receive a full written judgement before the end of the week and have until 14 July to appeal.
The RFL has stressed that it has taken more steps than any other governing body to crack down on homophobia having joined forces with gay rights charity Stonewall.
"Our sport is viewed by Stonewall as a model with the way it deals with issues around homosexuality," stated Ledger.
"In March 2009 we signed the Stonewall Charter to show our commitment towards these issues. The RFL is the only national governing body to have joined the Stonewall diversity programme which raises awareness over diversity issues."
Ledger also warned that the fans' behaviour could cost the club its Super League status.
"The behaviour of club supporters is one of our considerations in the licensing process," he said.
"It would be wrong to say Castleford getting a licence or not may hinge on this but the fans need to be aware they are doing the club no favours. This kind of behaviour would not get a favourable tick in the RFL's consideration of Super League licences."