Echoing criticism from the UK, Canada and Australia, the US state department urged Egypt to "redress the verdict".
The reporters, Canadian-Egyptian Mohamed Fahmy, Egyptian Baher Mohamed and Australian Peter Greste, were convicted of "spreading false news".
Mr Greste was deported to Australia this year and was tried in absentia.
State department spokesman John Kirby said in a statement: "We urge the government of Egypt to take all available measures to redress this verdict, which undermines the very freedom of expression necessary for stability and development.
"The freedom of the press to investigate, report, and comment - even when its perspective is unpopular or disputed - is fundamental to any free society and essential to democratic development."
Australia's Minister for Foreign Affairs Julie Bishop said she was "dismayed" by the sentences.
Ms Bishop said she had spoken with Mr Greste and would "continue to pursue all diplomatic avenue with my Egyptian counterpart" to clear Mr Greste's name.
Reaction: Peter Greste speaks to the BBC
On Sunday, Mr Greste said again that he was innocent.
"There was never any evidence to confirm any of the allegations against us," he said.
"We will continue to fight this, using any available means open to us. This is a matter of natural justice."
The UK Minister for the Middle East and North Africa Tobias Ellwood said: "I am deeply concerned by the sentences handed down today against journalists in Egypt.
"These sentences will undermine confidence in Egypt's progress towards strong long-term stability based on implementing the rights granted by the Egyptian constitution."
Canada demanded Mr Fahmy's "full and immediate release".
Mr Fahmy's lawyer, Amal Clooney, called on Egypt's President Abdul Fattah al-Sisi to issue a pardon to the journalists.
"The verdict today sends a very dangerous message in Egypt," she told reporters. "It sends a message that journalists can be locked up for simply doing their job, for telling the truth and reporting the news."
She said she would push for her client, who has given up his Egyptian citizenship, to be deported to Canada.
The three journalists are accused of aiding the banned Muslim Brotherhood group but they strenuously deny the allegations.
They 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.
Mr Greste's lawyer, Chris Flynn, said the men's re-trial "was a sham and was miscarried at every step".
He also urged President Abdul Fattah al-Sisi to intervene.
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.

The Terriers made 10 changes for the trip to St Andrew's having sealed a Championship play-off place, but the EFL said the result would stand.
Blackburn boss Tony Mowbray later questioned Town's line-up.
Rovers, who occupy the final relegation place, are two points behind Harry Redknapp's Blues with one game to play.
The EFL said in a statement: "We have today written to Huddersfield Town to request their observations in relation to team selection during their recent Championship match with Birmingham City and, as per our regulations, the EFL executive will refer the matter to the board if it is deemed appropriate to do so.
"It should be noted, however, that the result of Saturday's game will stand in all circumstances and any potential action would be taken against Huddersfield Town directly."
Blackpool and Wolves were fined for fielding much-changed teams in Premier League matches in 2010 and 2009 respectively.
Earlier this season 12 League One and Two teams were fined for playing weakened sides in the Checkatrade Trophy, although that competition had specific regulations regarding team selection.
The US has said it is "deeply disappointed and concerned" at the three-year jail sentences passed in Egypt on three al-Jazeera journalists.
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The EFL has written to Huddersfield to "request their observations regarding team selection" for Saturday's 2-0 defeat by Birmingham City.