Maharashtra minister Jitendra Awhad of NCP joined the students at the overnight protest and sat with them for a while. "When people fear intellect, there is anarchy," the minister told reporters.
NCP chief Sharad Pawar said JNU students were subjected to a cowardly and planned attack.
"JNU students and professors were subjected to a cowardly but planned attack," he said. "Use of violent means to suppress democratic values and thought will never succeed," Pawar added.
Asserting that students in Maharashtra were safe, Thackeray said he will not tolerate any move to hurt them.
"The attack on JNU students on Sunday night reminded me of the 26/11 Mumbai terror attack. I will not allow anything like JNU to happen here in Maharashtra...students are feeling unsafe in the country," he told reporters here.
Terming the masked attackers at JNU as "cowards", Thackeray said their identity should be revealed.
"If Delhi Police fail to find out perpetrators of the attack, then they will also be in the dock," he said.
At the Gateway of India in south Mumbai, students shouted slogans condemning the violence.
After the protest began on Sunday midnight, a group of students held a candlelight vigil to show solidarity with the JNU students.
Youngsters, mostly students from different colleges in Mumbai, assembled on pavement across the Taj Mahal Palace Hotel near the Gateway of India to condemn the violence.
It was an "impromptu assembly at a short notice", a student said.
Meanwhile, NCP workers staged a protest outside the BJP office in Mumbai to show solidarity with JNU students.
They shouted slogans against Home Minister Amit Shah. They were taken into custody, police said.
Violence broke out in JNU on Sunday night as masked men armed with sticks and rods attacked students and teachers and damaged property on the campus.