The disqualification was a result of "unfair means" resorted by the students as they had changed their responses on the answer sheets by scratching or using white fluid.
The decision, however, led to resentment and protest from the affected students, eventually prompting UGC to change its decision.
According to UGC, more than 21,000 students were disqualified.
"... In view of large number of students representing that disqualification clause was not specifically mentioned in the guidelines/instructions, it has now been decided to process such result by deducting the marks of those responses which were changed by scratching or using white fluid," UGC said in a statement.
UGC, however, warned that in future NET examinations, the candidates are liable to be disqualified in case responses are changed by scratching or using white fluid.