This week Mr Ghanimat, 45, with seven children, was sentenced to only three months in prison, a tacit admission by the prosecutor that he had committed no serious offence.
Human rights lawyers say his case proves that Palestinian prisoners are routinely tortured by the Israeli security forces and not only when they are suspected of knowing of an attack.
"It was the worst case of torture I have seen in Israel," says Allegra Pacheco, Mr Ghanimat's lawyer, who saw him in the Russian compound prison in Jerusalem after eight weeks of continuous interrogation.
"His hands and legs had swelled to bubbles because there were tight handcuffs on both. There were gashes on his arms and some of them were pussy and bleeding."
Mr Ghanimat was arrested in the village of Tzurif, north of Hebron, on 10 April after Israeli security (Shin Bet) rounded up a cell of Izzedin Kassam, the military arm of the militant Islamic group Hamas.
The cell was responsible for planting a bomb in a cafe in Tel Aviv in which three women were killed. Mr Ghanimat had the same last name as the bomber, but was not related to him (though the Israeli press reported that he was his brother).
Israeli security is usually careful to use methods of torture which do not use marks.
In Mr Ghanimat's case they were less inhibited. Ms Pacheco, who works for LAW, a Palestinian human rights group, says this may have been because he did not at first have a lawyer.
Always tightly handcuffed, so blood could not reach his hands, a dirty sack placed over his head and deprived of sleep for long periods, he says he was kicked and beaten until he could not walk.
In a painfully written affidavit on 27 May, the first time he saw his lawyer, Mr Ghanimat wrote how one of his interrogators called "Captain Tariq" sat "on a small chair, placed it on my chest ... and jumped from the chair onto my chest causing me severe pain." Another, called "the Major," pulled me "from under the chair, which caused injuries to my legs".
Although he screamed with pain continually and was bleeding, a prison doctor who saw him prescribed only the equivalent of Vicks for his chest.
During his interrogation, Mr Ghanimat was continually asked to confess to being a member of Izzedin Kassam. Desperate to end the torture he admitted that in 1994 an Israeli had come to Tzurif with a stolen car in which he and a friend had found a gun. They hid it and the friend had later handed over the weapon to Palestinian security.
His interrogators seemed uninterested in this.
Mr Ghanimat says one of them said to him: "Torture is like the waves of the sea - that which is to come is more severe than that which has passed."
Shocked by what she had seen, Ms Pacheco appealed to the Israeli High Court under its president Aharon Barak to ask for a court order to stop the torture. The court allowed Mr Ghanimat to come to court and show his wounds. Photographers were allowed to photograph them. At first Mr Ghanimat would not speak in front of Shin Bet interrogators, saying: "I can't. They'll kill me when we get back to prison." Mr Barak then told the Shin Bet officers to leave the court.
After Mr Ghanimat described what had happened the State Attorney said that "at this stage" no more physical pressure would be placed on him. He returned to the Russian Compound where the Shin Bet made him write out a confession about the gun in the stolen car, a technical offence for which he has just received three months in prison. He is to be released on 9 July.
In May the UN Committee against Torture decided that Israel, by permitting its security forces to use "moderate physical pressure" against prisoners, legalises torture.
It singled out seven methods of interrogation, such as the use of cold air to chill prisoners, sleep deprivation, sacks over the head, shackling in painful positions and, violent shaking (which has the same effect as a whiplash injury in a car crash) as breaching the UN Convention against Torture.