Bassam and Ghassan Nabulsi, former business partners of Sheikh Issa, who filmed and kept the video tape, were sentenced in absentia to five years each in prison.
The video tape was handed to the ABC News channel last April.
Sheikh Issa was charged with rape, endangering a life and causing bodily harm, the Gulf National newspaper reported.
The torture victim was identified by Nabulsi as an Afghan grain dealer, Mohammed Shah Poor, who the sheikh accused of short changing him on a grain delivery to his royal ranch on the outskirts of Abu Dhabi.
Al-Mulla said that Sheikh Issa, who has been in detention for the past seven months, would be released following the acquittal.
Sheikh Issa's lawyer said that he was on a high amount of medication and that he was also drugged by the Nabulsi brothers.
| Sheikh Issa was in a drugged state when the incident occurred, his lawyer claimed [AFP]
He told the court they had orchestrated the incident and filmed it to use as blackmail, the National
A forensic medicine expert told the court in the previous hearing that the medication Sheikh Issa was on could "cause anger, suicide, violence, depression and loss of memory".
Six other defendants faced charges for the 2004 incident, which took place in the oasis city of Al Ain.
Two of them were ordered to pay a "temporary compensation" of 10,000 dirhams ($2,724) to the Afghan, who can file a new lawsuit to claim full compensation, the lawyer added.
Three others employed at the farm where the torture took place were sentenced to between one and three years in jail. A guard at the farm was acquitted.
The tape shows Sheikh Issa viciously beating a worker in an empty stretch of the desert.
A man in a UAE police uniform is seen on the tape tying the victim's arms and legs, and later holding him down as the Sheikh pours salt on the man's wounds and then drives over him with his Mercedes SUV.
In a statement to ABC News in April, the UAE ministry of the interior said it had reviewed the tape and acknowledged the involvement of Sheikh Issa.
"The incidents depicted in the video tapes were not part of a pattern of behaviour," the interior ministry's statement said.
The government statement said its review found "all rules, policies and procedures were followed correctly by the police department".
Nabulsi is now suing the sheikh in federal court in Houston, Texas, where he resides, alleging he also was tortured by UAE police when he refused to turn over the tape to the sheikh following their falling out.
"They were my security, really, to make my case that this man is capable of doing what I say he can do," Nabulsi said in an ABC interview in April.
Nabulsi said Sheikh Issa ordered the recording of the tape because he liked to watch the torture sessions later in his royal palace.