The expulsion was carried out after taking into account their mercy plea which was rejected by the institute's apex academic body.
During the admission, the parents had signed declaration that the poor performance could lead to expulsion of the students, IIT Roorkee officials said.
The institute had warned the students in May to pull up their socks, after the second semester exams, and they were given time to file a mercy appeal
HRD Ministry officials maintained silence over the episode, saying the IITs are autonomous bodies, governed by their own rules.
A professor of an IIT also raised questions over the revamped IIT-JEE entrance test which makes it "relatively easier" for a student to crack the objective type questions if "luck favours him".
Officials recalled receiving pleas from students directly for leniency whose CGPA was less than five.