Thornton's pleas for a free pardon or remission of her sentence were also rejected by Michael Howard, who said pardons were only for the innocent and remissions granted only in 'most exceptional' circumstances.
Thornton, now 37, had sought the help of friends, her GP and solicitor, the police, Alcoholics Anonymous and a psychiatrist specialising in alcohol abuse before she killed her husband, Malcolm, a former policeman, on 14 June 1989. She stabbed him in the stomach with a kitchen knife as he lay on a sofa after a drinking bout and a row. She was jailed for life in February 1990. Seventeen months later, her appeal - on the grounds that her husband's violent behaviour had provoked the killing - failed.
The case raised public awareness of domestic violence and the shortages of refuges and care for its victims, and questioned whether the legal defences, particularly the law on provocation, was better suited to a man's immediate rage than a woman's slow build-up to breaking point.
There followed the successful appeals of Kiranjit Ahluwalia, Janet Gardner and Amelia Rossiter. And in the crown courts, Pamela Sainsbury, who strangled her violent husband, and June Scotland, who battered hers to death, were both given probation.
Yesterday, Sandra Horley, of Chiswick women's refuge, said: 'It seems that justice for battered women is going to remain a lottery. This decision highlights the need to establish a new defence for battered women.'
She also echoed the calls from senior judiciary, including Lord Taylor, the Lord Chief Justice, to abolish the mandatory life sentence for murder, so that the courts could reflect some sympathy for battered women.
Julie Bindle, of Justice for Women, which led the campaign for Thornton's freedom, said: 'It is outrageous that the Home Secretary has taken this cowardly decision.
'It is obvious that he has no understanding of the issues of violence against women and further proves that our homicide defences do not fit women's experiences.'
Thornton's call for a fresh appeal was based on new psychiatric evidence that her state of mind had been affected by the violence she had suffered and that she had been provoked.
Mr Howard said he had given her case 'comprehensive consideration', but added: 'I have, however, concluded that, on presently available information, I would not be justified in referring the case to the Court of Appeal, or in recommending the exercise of the Royal Prerogative of Mercy, either to grant a Free Pardon or to remit the remainder of her sentence.'
Last night, Thornton, who is in Bullwood Hall prison, Essex, promised to continue her campaign. She said: 'This is obviously a political decision and has nothing whatsoever to do with justice.'