The trees, part of a green strip known as Aarey colony, were being cut to make way for a new metro rail project.
Locals have long opposed the move, and filed petitions seeking Aarey to be declared a protected area.
But a high court dismissed the petitions on Friday, sparking protests as officials began felling the trees.
They planned to cut 2,185 trees, and admitted in the Supreme Court that more than 1,500 had already been cut. But petitioners claim that officials have cut around 2,500 trees.
The fight to save Mumbai's last 'green lung'
Local residents, students and environmental activists clashed with police on Friday as they took to the streets to stop authorities, and even broke through barricades to enter Aarey colony. More than 50 people were arrested and police imposed restrictions on public gatherings.
The protests grabbed the national spotlight over the weekend, and the Supreme Court took suo moto (without a formal complaint from any party) notice.
A special two-judge bench heard the matter on Monday after students wrote to the chief justice, asking the court to intervene and save the trees.
The court asked the state government of Maharashtra, where Mumbai is located, to not cut any more trees.
The court also asked the government to maintain "status quo" - which means that no construction can take place - until 21 October when it will hear the matter again.
The court also ordered the release of all activists who were arrested or detained on bail.
What is Aarey colony?
Spread over 1,300 hectares (3,212 acres), Aarey is a densely forested area dotted with lakes and has the Mithi river flowing through it. It lies at the heart of Mumbai and is often referred to as its last green lung.
It's locally known as the Aarey "milk colony" because most of the land was given to the department of dairy development in 1951. But they are allowed to grow cattle fodder only on a fraction of the land.
Earlier this year, officials cleared some 40 hectares of the forested area to build a zoo, complete with a night safari. And now, locals complain, another slice of it is in danger from the metro construction.
They also fear that the government will eventually clear the way for private builders to encroach on the Sanjay Gandhi National Park, which lies to the north of Aarey colony.
Officials, however, dismiss these fears as unfounded and point out that the construction for the metro only requires 30 hectares.
How crucial is the metro rail for Mumbai?
The city badly needs a "mass rapid transport system," Ashwini Bhide, managing director of the Mumbai metro rail corporation, had told the BBC earlier.
The land in Aarey colony, she said, was "the most suitable land due to its size, shape and location". BBC