The bill was adopted by 413 votes to 226.
The vote took place two months after the member states and the European Parliament agreed on the goals, which themselves followed the COP30 climate summit in Brazil.
The draft allows measures that reduce emissions in countries outside the EU to be counted for up to 5 percentage points of the 90 percent. It also means the extension of the EU's emissions trading system to the construction and road transport sectors is postponed from 2027 to 2028.
The EU's goal has long been to achieve climate neutrality by 2050.
