The leaders voted by 27 to one at a summit in Brussels to give ex-Polish premier Tusk a new two-and-a-half-year mandate with only Poland voting against.
Poland's eurosceptic right-wing government, a bitter long-term foe of the centrist Tusk, reacted furiously to the decision and was set to block the summit's final communique in a show of pique.
Tusk thanked the leaders for their support and vowed that he would "do my best to make the EU better" as it tries to build unity in the wake of Britain's shock decision to leave.
Polish Prime Minister Beata Szydlo, of the conservative Law and Justice Party, was the only one not to raise her hand during the vote, for which Tusk had to leave the summit room, officials said.
"It may sound like a paradox because of the context, but anyway your decision is an expression of our unity today," Tusk told the leaders, who applauded after he was brought back in after the vote.
But the decision threatens a deep rift with the largest of the eastern post-Soviet EU states, just weeks before the bloc had hoped to make a show of unity at its 60th birthday celebrations.
"We know that this is now a Union under Berlin's diktat," Poland's Foreign Minister Witold Waszczykowski was quoted as saying Thursday after the vote. "A very toxic union, that could harm many countries."
Poland to block communique
In a show of protest, Poland now intended to veto the official summit conclusions that the EU leaders are supposed to issue at the end of the meeting, European sources told AFP.
The conclusions were meant to cover the economy, defence, and unrest in the Balkans -- and Tusk's re-election, although the block will not have any effect on that, the sources said.
Szydlo had said it was a "question of principles" that the head of the European Council -- which groups the leaders of the bloc's 28 member states and organises summits -- should be backed by their home country.
"Poland will defend these founding principles of the EU until the end. Countries that don't understand that are not building European society, they are destabilising it," she said.
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Poland, which has repeatedly rowed with Brussels in recent months over political reforms, put forward a surprise rival candidate to Tusk, euro-MP Jacek Saryusz-Wolski, at the weekend.
Tusk has been a long-term foe of the head of the conservative Law and Justice party, Jaroslaw Kaczynski, who has accused him of "moral responsibility" for his twin brother's death in a plane crash in Russia in 2010, when Tusk was prime minister.
Tusk however had the overwhelming support not only of Germany but even of Poland's traditional eastern European allies like Hungary which share a similar eurosceptic outlook.
"She (Szydlo) is pouting," one diplomat quipped.
Merkel, Europe's most powerful leader, had supported Tusk's re-election as a "sign of stability" after he steered Europe through tensions with Russia, the Greek debt crisis and Britain's vote to leave the bloc.
British Prime Minister Theresa May had "actively supported him" and was "pleased he's re-elected" a Downing Street spokesman said.
Clouds over Rome
The row threatens to cloud a summit in Rome on March 25th to mark the 60th anniversary of the EU's founding treaty, at which the EU hopes to unveil a declaration of unity in the wake of Brexit.
On Friday the 27 EU leaders without Britain's May will look at preparations for the Rome meeting, a ceremonial occasion which will include a meeting with Pope Francis.
But that too threatens to highlight the divisions in the EU, already battered by Brexit and the election of an apparently hostile Donald Trump as US president.
There is disagreement over whether plans for a major declaration on the bloc's next 10 years, to be made in Rome, should include a mention of plans for a so-called "multi-speed Europe."
The leaders of the EU's post-Brexit "big four" -- Germany, France, Italy and Spain -- used a summit in Versailles on Monday to back plans for countries to choose at which speed they integrate on key issues.
But eastern countries in particular fear this will lead to a virtual apartheid system where they are left behind on issues like the euro currency, the economy and defence while the major powers push ahead.
