The student activists were demanding restoration of the students union, which was dissolved in 2007, and removal of senior University officials whom they blamed for rusticating more than 150 students during the past three years.
They had been holding a sit-in outside the official residence of Vice Chancellor P K Abdul Azis for more than two months to press for their demands.
Spokesman of the student protesters Mushtaq Ahmad announced their decision to end the protest in the presence of the Vice Chancellor and top district officials at the sit-in site shortly after midnight.
The decision came following the announcement made by the Vice Chancellor that all major demands of the students had been agreed to.
In a statement, University authorities agreed to start the election process from January 3, 2011.
"Elections for the students' union and also for the ten student representatives from different faculties to the University Court will be held on the basis of recommendations of the Lyngdoh Committee," the statement said.
The suspension order against five student protesters who had been leading the current agitation would also be withdrawn, the authorities said, adding, no further action will be taken against any student who participated in the current agitation.
The Vice Chancellor, who had vacated his official residence due to the continued sit-in by the agitating students outside his house and was staying in a government rest house, finally returned to his lodge after 70 days of self-enforced exile.
Mushtaq Ahmad told mediapersons today, "We are grateful to the Members of Parliament especially those who are members of the University Court and some prominent alumni who have given us unstinted support for restoration of our democratic rights."
Former MP and elected member of the University Court Wasim Ahmed, who played a major role in resolving the present crisis, welcomed the ending of the impasse.
Meanwhile, the AMU Teachers' Association has passed a resolution urging Justice A N Divecha, a member of the enquiry panel which is probing corruption charges against senior AMU officials, to not resign from the panel.
The teachers have also called upon the Visitor of the University President Pratibha Patil to ensure that the Vice Chancellor, who is facing corruption charges, "is not allowed to influence the proceedings."