The apex court bench headed by Justice Dipak Misra vacated its stay ordered last Friday, but asked the high courts not to interfere in the petitions regarding counselling and admission to the IITs to avoid any confusion.
Counselling is a process in which a candidate, who clears the entrance examination, chooses the best college and stream according to his or her choice based on their rank.
The bench, also comprising Justices A M Khanwilkar and M M Shantanagoudar, asked the IITs to give an undertaking that such mistakes will not recur and make sure that no situation in which bonus marks have to be awarded arose in future.
Attorney General K K Venugopal, representing the IITs, said such a situation will not arise in future.
The bench said the 2005 judgement in Guru Nanak University case will not apply in the present matter as there were a huge number of students involved and there was a system of negative marking in the exam.
The apex court also noted that an experts' body of IITs had met twice to decide that bonus marks should be awarded across the board for the wrong questions.
The Supreme Court had on July 7 restrained the IITs from conducting further counselling and admissions saying the court will go by its earlier judgement of 2005 and bonus marks cannot be given to those who have not attempted the wrong questions.
The AG had, however, pointed out that there was negative marking for every unsuccessful question and there may be some students who had opted not to answer "the said vague questions fearing negative marking".
Therefore, across the board bonus marks were given to the candidates, Mr Venugopal had told the court, adding that otherwise the IITs would have to strike down the marks.
The AG had also said that it was difficult to re-evaluate the answersheets of over two lakh students who took the examination and awarding of bonus marks across board was the most practical solution.
The apex court had on June 30 issued notice to the Ministry of Human Resource Development on a plea seeking quashing of the IIT-JEE 2017 rank list.
The petition, filed by an IIT aspirant Aishwarya Agarwal, had sought the court's direction to declare that the action of awarding bonus marks to candidates who had appeared in the JEE (Advanced)- 2017 examination was wrong and violated her right, as well as that of other students.
Since then several other students had approached the apex court seeking quashing of rank list.
Several IIT aspirants in their pleas had sought a direction for preparation of the all-India rank list after rectifying the scores of JEE (Advanced) and also award marks for the incorrect questions to the candidates who had attempted the right answers.