The Czech Republic and Hungary eventually dropped their resistance after winning a guarantee that nuclear energy would be recognised as a way for EU states to reduce greenhouse gas emissions. But Poland remained against.
The tussle came a day after Germany's Ursula von der Leyen, the new head of the bloc's executive European Commission, proposed a 100-billion-euro ($110 billion) investment plan for net-zero greenhouse gas emissions by mid-century, declaring it Europe's "man on the moon moment".
With fires, floods and droughts ruining millions of lives around the world, the European Union's new push comes as popular protest demanding more action to fight climate change spreads around the bloc.
Von der Leyen said the Brussels summit deal, reached in the wee hours of Friday by 27 national EU leaders, was enough for the commission to start rolling out concrete climate legislative proposals for the bloc next year based on the 2050 goal.
"We acknowledge that the transition is a big one for Poland," she said. "It needs more time to go through the details, but this will not change the time frame ... for the commission."
Polish Prime Minister Mateusz Morawiecki, whose country relies on highly polluting coal for some 80% of its energy needs, said the negotiations had been "very difficult". "Poland will be reaching climate neutrality at its own pace," he told reporters after the marathon talks.
German Chancellor Angela Merkel said she was satisfied with the outcome. "There is no splitting of Europe into separate parts but one member state needing more time to see how it will be implemented," she said.