The Big Brother contestant is alleged to have told the player that she would go to the press about their six-month affair if he did not adhere to the demands.
Thomas argued that she has effectively been "gagged" from revealing her side of the story since the star has taken out an injunction preventing the disclosure of his identity.
On Monday, Mr Justice Eady refused a joint bid by Thomas and The Sun newspaper to overturn the high-profile footballer's privacy injunction.
Eady said there was "ample reason not to trust" Thomas, and insisted that the evidence before the court on April 14 "appeared strongly to suggest that the claimant (the anonymous footballer) was being blackmailed".
The footballer accused Thomas of repeatedly demanding £50,000 from him in March. He agreed to meet her "in a hotel where he was staying" in April. There he gave her "a signed football shirt" but said that he was not prepared to give her "the sum of £50,000".
She asked to see him again shortly afterwards to which "he agreed with reluctance" and provided her with some football tickets. Although the position was "by no means clear", Mr Justice Eady said that he believed evidence "appeared to suggest" that the reality TV star arranged two hotel meetings with the player apparently "in collaboration with photographers and/or journalists".
The player claimed that on April 13, he texted Thomas to say that he might be willing to offer her some money after all but Thomas allegedly increased the amount to £100,000.
Eady added: "The majority of cases over the last few years ... would appear to be of the so-called 'kiss and tell' variety and they not infrequently involve blackmailing threats. Blackmail is, of course, a crime and in that context the courts have long afforded anonymity to those targeted as a matter of public policy. This has not hitherto been questioned."
Following the ruling on Monday, in a statement on behalf of Thomas by her lawyer, she revealed that she was "stunned" with how she was portrayed in the ruling.
She commented: "What's more I can't even defend myself because I have been gagged. Where is the fairness in this? What about my reputation? If this is the way privacy injunctions are supposed to work there is something seriously wrong with the law."