"We Are Preserving Our Shared Home," read one demonstrator's placard. Netanyahu was guilty of a "legal putsch", said another.
Israeli media put the number in attendance at around 80,000, with thousands more at protests in Jerusalem and Haifa.
The 73-year-old premier on Friday signalled flexibility on the reform plan, saying it would be implemented "with careful consideration while hearing all of the positions".
Polls have diverged on public views of the reforms. Channel 13 TV last week found 53% of Israelis were opposed to changing the court appointments' structure while 35% were in support. But Channel 14 TV on Thursday found 61% in favour and 35% opposed.
Critics of the Supreme Court say it is overreaching and unrepresentative of the electorate. Its proponents call the court a means of bringing equilibrium to a fractious society.
"Tens of thousands of people were at tonight's demonstrations. In the election held here two and a half months ago, millions turned out," tweeted Miki Zohar a senior lawmaker in Netanyahu's conservative Likud party.
"We promised the people change, we promised governance, we promised reforms - and we will make good on that."
