He also said he hoped President Andrzej Duda would quickly sign the newly approved reform into law.
Last week, both houses of parliament adopted two other contested pieces of judicial legislation, including a bill stating that the justice minister will name the chief justices of Poland's common courts.
Thousands have taken took to the streets in opposition to the proposed judicial changes in Poland, accusing Law and Justice of aiming to stack courts with its own candidates and to dismantle the rule of law.
The legislation calls for firing current Supreme Court judges, except those approved by the president, and it gives the president power to regulate the courts.
Saying that the laws "would increase the systemic threat to the rule of law in Poland", the Commission urged Poland's leaders to hold off on making any changes and return to talks with the European Union that have been going on since January of 2016.
Opposition supporters shout slogans and raise candles as they protest in front of the Supreme Court, seen in the background, against a law on court control in Warsaw, Poland, Friday, July 21, 2017.
Thousands turn out to rally against new bill allowing parliament to appoint supreme court, with European Union also voicing concern.
European Union officials disagree, and if the Supreme Court measure goes into effect, it could trigger an effort in Brussels to strip Poland of its voting rights in decisions of the bloc - a never-invoked nuclear option.
The commission also urged the Polish government to put its new laws on hold.
Beata Szydlo said Thursday night that the legislation was a result of public criticism of the legal system's inefficiency and blamed the public outcry it has triggered on the "frustration" of the opposition. Thus, the government wants to get rid of the pathologies in the judicial system of the country. The bill was not subject to any public consultation and was passed by the lower chamber just nine days after it was first submitted.
European Union president, Donald Tusk, Poland's former prime minister, has appealed to President Andrzej Duda for a meeting to seek ways out of the situation that, he said, goes against EU values and is destructive to Poland's global image.
In Trump's troubling and odd speech in Poland two weeks ago, the US president said he was honored "to address the Polish nation that so many generations have dreamed of: a Poland that is safe, strong, and free". Critics say it kills judicial independence and violates the rule of law.
Opponents of the move argue that it will demolish judicial independence and separation of powers in the country, marking a major shift for a ruling government that has already been accused of pursuing an illiberal agenda.
Ideally, therefore, victory needs to be won by the people of Poland, supported by democrats and progressives everywhere.
While PiS remains broadly popular among many Poles, particularly poorer and older voters from the countryside, there have been widespread protests against the plans.