Egyptian Baher Mohamed, Canadian Mohamed Fahmy and Australian Peter Greste were all handed three year jail sentences when the court delivered the verdict on Saturday, sparking worldwide condemnation of the decision.
Mohamed was sentenced to an additional six months for possession of a spent bullet casing.
Judge Hassan Farid, in his ruling, said he sentenced the men to prison because they had not registered with the country's journalist syndicate.
He also said the men brought in equipment without security officials' approval, had broadcast "false news" on Al Jazeera and used a hotel as a broadcasting point without permission.
The verdict was immediately slammed by Al Jazeera Media Network's Acting Director General Dr Mostefa Souag, who said: " Today's verdict defies logic and common sense . Our colleagues Baher Mohamed and Mohamed Fahmy will now have to return to prison, and Peter Greste is sentenced in absentia.
"The whole case has been heavily politicised and has not been conducted in a free and fair manner."
Dr Souag said, "There is no evidence proving that our colleagues in any way fabricated news or aided and abetted terrorist organisations and at no point during the long drawn out retrial did any of the unfounded allegations stand up to scrutiny.
"A report issued by a technical committee assigned by the court in Egypt contradicted the accusations made by the public prosecutor and stated in its report that the seized videos were not fabricated.
Source: Bloom Gist, Agencies