Canadian-Egyptian Mohamed Fahmy and Egyptian Baher Mohamed were led away from court after the verdict. Australian Peter Greste was deported back to Australia earlier this year and was on trial again in absentia.
The three are accused of aiding the banned Muslim Brotherhood group but they strenuously deny the allegations. The three journalists were originally sentenced in July 2014, with Mr Greste and Mr Fahmy receiving seven years and Mr Mohamed getting 10 years.
But their convictions were overturned in January this year and they were freed in February to await retrial.
Giving the verdict on Saturday, judge Hassan Farid said the three men were not registered journalists and had been operating from a Cairo hotel without a licence. He handed three-year sentences to Mr Greste and Mr Fahmy but gave Mr Mohamed an additional six months.
It is unclear how long Mr Fahmy and Mr Mohamed will now serve. They were in prison for about a year before being freed.
Lawyers for the three journalists are expected to appeal the decision.
The BBC’s Lyse Doucet, who was in the court, said the verdict came as a shock to a room packed full of Egyptian and foreign journalists.
The expectation was that the journalists would be found guilty, she adds, but that they would be given a lesser sentence and be allowed to walk free.