The Polish government insisted Mr Tusk, a former PM from a rival party, had violated his mandate by interfering in domestic politics.
Mr Tusk is expected to play a major role in the UK's Brexit negotiations.
After his re-election he tweeted: "Grateful for trust & positive assessment by #EUCO [European Council]. I will do my best to make the EU better."
Polish Prime Minister Beata Szydlo had strongly opposed Mr Tusk's candidacy and proposed another candidate, a little-known Polish MEP called Jacek Saryusz-Wolski.
She said after the vote that Mr Tusk's reappointment would damage EU efforts to recover after the UK's departure and that it was a "question of principles" that any candidate for the post should be backed by his home country.
"Poland will defend these founding principles of the EU until the end," she said, quoted by AFP news agency. "Countries that don't understand that are not building European society, they are destabilising it."
What is the UK's position?
There had been some suggestion that the UK might abstain from the vote to win Polish support over Brexit negotiations.
But ultimately all but Poland voted for Mr Tusk, and the Press Association news agency quoted UK government sources as saying Prime Minister Theresa May was "pleased" he had been re-elected.
Thursday's meeting of EU leaders in Brussels is the last that Mrs May will attend before formally launching the two-year Brexit process later this month.
Although Brexit itself is not on the agenda, leaders will meet again on Friday - minus Mrs May - to discuss EU unity.
Why is the Polish government so hostile to Mr Tusk?
Mr Tusk was prime minister from 2007-2014. He led the centre-right Civic Platform when the PiS was in opposition.
PiS leader Jaroslaw Kaczynski holds Mr Tusk "politically" responsible for the 2010 plane crash in Russia which killed his twin Lech Kaczynski, the then Poland's president, and all other 95 people on board.
The plane crashed in dense fog. Official investigations ruled pilot error was the principal cause.
In 2012, Jaroslaw Kaczynski told Mr Tusk in parliament: "In the political sense you bear 100% responsibility for the catastrophe in Smolensk."
Many Poles believe Mr Tusk's government did not do enough to explain the causes of the crash. Critics say Mr Tusk should not have allowed the Russians to conduct the first crash investigation.
Under the Chicago Convention, which covers international air travel, the state on whose territory a crash occurs bears responsibility for conducting the investigation.
Jaroslaw Kaczynski also accused Mr Tusk of favouring "solutions that are extremely harmful to Poland".
What does the European Council president do?
The European Council brings together the heads of state and government of the 28 EU member states. Jointly they set the EU's strategic direction in key areas, such as reform of the eurozone, the Greek debt crisis, the migrant challenge and relations with Russia.
The Council president aims to achieve consensus - deploying all his diplomatic skills - on these tricky issues, where national tensions often dictate how leaders behave.
Mr Tusk's first term ends on 31 May, and he will now stay in office until 30 November 2019. That period coincides with the expected two-year Brexit talks on UK withdrawal from the EU.
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