The poll result assumes significance as Delhi assembly election is due in November.
Twelve candidates each for the posts of president and vice president, 17 for the post of secretary, and 10 for joint secretary were in the fray for the four major posts of DUSU.
The campaign this time was dominated by issues such as women security and the new four-year undergraduate programme.
The drubbing for NSUI came just a year after it had swept the students union polls, by winning all three top posts.
Karishma Thakur of National Students Union of India (NSUI) has been elected as the secretary.
Akhil Bharatiya Vidyarthi Parishad (ABVP) candidate Aman Awana and Utkarsh Chaudhary were elected as president and vice-president respectively. Raju Rawat, also of ABVP, was elected as the joint secretary.
BJP students' wing ABVP on Saturday wrested control of Delhi University Students Union from Congress' ABVP, winning three out of the four top posts.