However, it transferred Kanhaiya Kumar's bail plea to the Delhi high court, saying that the atmosphere in the trial court was "not proper".
Mr Kumar was attacked in the court premises by slogan-shouting lawyers.
His lawyers told the top court that they feared for his safety.
Mr Kumar, the student union leader from Delhi's prestigious Jawaharlal Nehru University (JNU) was arrested after a rally against the 2013 hanging of Mohammed Afzal Guru at which anti-India slogans were allegedly raised.
Afzal Guru was convicted over a 2001 plot to attack India's parliament - charges he always denied.
The attack was carried out by Kashmiri militants and left 14 people dead.
At Friday morning's hearing, the Supreme Court said it would tell the high court to take up the bail hearing quickly.
It also asked the Indian government and the Delhi police to ensure that adequate security was put in place at the high court to ensure Mr Kumar's safety.
Wednesday's attack on Mr Kumar in the Patiala house court had taken place despite the Supreme Court laying down strict guidelines after a previous hearing into the case also turned violent.
Meanwhile, thousands of people across India marched on Thursday to protest against Mr Kumar's arrest.
Organisers said about 10,000 people gathered in the capital, Delhi.
Protests have also spread to other universities across the country. Students from the southern city of Chennai (Madras) clashed with the police on Thursday morning, while agitations in a top university in the eastern city of Kolkata (Calcutta) turned violent.
Political parties have also joined the fray, with opposition groups condemning the government action.
However, angry government ministers have not backed down, and vowed to punish the "anti-national elements".
India's top court has declined to hear a bail plea of a student leader charged with sedition, saying that to do so would send the message that lower courts were "incapable".