Fee Review Committee chairman Alok Ghosh said the resignation letter was sent to the Chancellor through a messenger from the university in Nadia district this morning.
Hangloo had resigned for the first time on October one but it was "not accepted" by the Governor and State Education minister Partha Chatterjee, who asked him to "go on with his work".
The VC had then resigned after he and other senior university officials and teachers were gheraoed for 19 hours, including the entire night by post-graduate students in his office along with the university registrar, dean of students welfare and finance officer.
Earlier in the day the university decided to revoke the fee hike decision as demanded by students.
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Ghosh said the university will roll back the fee hike and bring it to the 2013-14 level for post-graduate students.
The four-member fee review committee had passed on the recommendation to the VC's office and announced the roll back following its nod.
The campus had been on the boil since February this year with students and non-teaching staff gheraoing the faculty and VC on several occasions on the fee issue as well as against some other measures taken by Hangloo.