The bill, proposed by the ruling Law and Justice (PiS) party, needs to be signed by President Andrzej Duda, an ally of PiS.
Fifty-five senators voted for the new measures while 23 voted against.
It was met with boos from protesters gathered in front of the Senate building. The U.S. Department of State voiced concern on Friday.
Law & Justice has been rushing through its reform, which would force into immediate retirement all Supreme Court judges with little or no debate and without consulting the judiciary.
PiS has offered no concessions, instead presenting the European Union criticism as unacceptable foreign meddling in the domestic affairs of the country, which overthrew communism in 1989 and joined the European Union in 2004. "We will not be intimidated by Polish and foreign defenders of the interests of the elite", Prime Minister Beata Szydlo said in an address on state television.
Under the current system, candidates for the Supreme Court are selected by an independent body consisting mainly of judges but also included a few politicians. It also introduces a disciplinary chamber that, on a motion from the justice minister, would handle suspected breaches of regulations or ethics.
Duda will meet Supreme Court President Malgorzata Gersdorf Monday, suggesting he won't make a decision before then. The head of state has 21 days to sign the document, veto it, or, if in doubt, submit it to the constitutional court.
Last week Poland's parliament passed two other government-backed bills which would allow the justice minister to appoint judges to the country's district and appeals courts, and a 60 percent parliamentary majority to nominate judges to an influential judicial ethics supervisory council.
"Authorities are tweaking laws to gain control over citizens and curb freedoms", Tusk said in an interview with broadcaster TVN24 on Friday.
The United States, Poland's most important ally in North Atlantic Treaty Organisation, issued a statement urging Poland to ensure any changes respect the constitution.
Tusk said in a statement that the PiS moves on courts were backwards, went "against European standards and values", harmed Poland's reputation and risked marginalising the country.
A senior aide to Duda, Krzysztof Szczerski, said Tusk should instead focus on explaining Poland's stance in Brussels. The opposition argues the measures amount to a "coup d'etat" but the PiS says the reforms are essential to rationalise the judicial system and fight corruption.
That rift is part of a greater divide within the bloc as governments including Poland, Czech Republic and Hungary come into conflict with Brussels as they embrace increasingly nationalist policies.
"If adopted, [the laws] would seriously erode the independence of the Polish judiciary", First Vice-President Frans Timmermans stated following the European Commission meeting earlier this week.
The European Commission has warned it could strip Poland of its European Union voting rights over the changes the government is making to the judiciary.
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