Alluni had been convicted in September 2005 on charges of collaborating with al-Qaeda.
The same court, however, had acquitted him of being a member of al-Qaeda.
Hours after the Supreme Court upheld Alluni's conviction, Al Jazeera said it was consulting its legal team to appeal against the ruling, to "ensure Alluni regains his freedom".
The Arab Committee for the Defence of Journalists described the move by the court as unjust and called upon all civil rights and media groups to "uncover the truth" of Alluni's case.
Concerns have been expressed about the health of Alluni who suffers from high blood pressure and problems with his spine.
Alluni gained international recognition as a journalist when he secured an interivew with Osama bin Laden, al-Qaeda's leader, in 1998, and for his coverage of the Afghanistan and Iraq wars.
Alluni was among 24 people tried in the High Court last year for belonging to al-Qaeda.
Eighteen were convicted, mostly of belonging to or cooperating with al-Qaeda.
Of those, three appeals were accepted by the Supreme Court on Thursday while the other 14 appeals were dismissed.
Yarkas' conspiracy conviction
Among those who succeeded in their appeal on Thursday was Imad Eddin Barakat Yarkas, said to be the leader of al-Qaeda in Spain.
Yarkas, known as Abu Dahdah, had been convicted of conspiracy to commit terrorist murder and sentenced to 27 years in jail. He will, however, continue to serve a 12 year sentence for leading "a terrorist group".
Three men in September's trial were accused of 2,973 murders in connection with the September 11 attacks on the United States but only Yarkas was convicted for conspiracy with the attackers.
The High Court ruled there was no proof that Syrian-born Yarkas took part in the attacks but said there was evidence he helped think up the plot, working with a cell in Hamburg.