The three -- Canadian national Mohammed Fahmy, Australian journalist Peter Greste and Egyptian producer Baher Mohammed -- were sentenced after a lengthy retrial.
At least three other co-defendants, accused of working with Al-Jazeera, received similar sentences.
All three were convicted last year on charges that included conspiring with the Muslim Brotherhood, spreading false news and endangering national security, but they have maintained their innocence, saying they were simply reporting the news.
The three journalists were originally sentenced to up to 10 years in prison. But their convictions were overturned in January this year and were freed in February to await retrial.
After today's verdict, Greste tweeted: "Shocked. Outraged. Angry. Upset. None of them convey how I feel right now. 3 yr sentences for @bahrooz, @MFFahmy11 and me is so wrong."
Al-Jazeera English acting director-general Mostefa Souag said the sentence "defies logic and common sense".
"The whole case has been heavily politicised and has not been conducted in a free and fair manner," Souag said.
Authorities arrested the trio and later charged them with allegedly being part of former President Mohammed Morsi's Muslim Brotherhood which was declared a terrorist organisation by authorities.
They were accused of airing falsified footage to damage national security.
The earlier verdict brought a landslide of international condemnation. The country's highest appeals court, later ordered their retrial, saying the initial proceedings were marred by violations of the defendants' rights.
Egypt deported Greste in February, though he remained charged in the case. Fahmy and Mohammed were released on bail.
The acting manager director of Al-Jazeera English, Giles Trendle, said that the verdict was "disgraceful, disgusting and we are shocked".
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