The Congress' student wing defeated BJP-led Akhil Bharatiya Vidyarthi Parishad (ABVP).
The annual elections were held after a gap of two years with over 22,000 students out of the total 36,115 students exercising their franchise.
NSUI's Hitesh Batra was elected general secretary of the university student union, defeating ABVP's Shubham Koul, while NSUI's Priyanka Patel won the election for vice president's post, defeating ABVP's Simran Modi.
In 2013, NSUI had won both the seats for the first time in nine years, but no elections were held in 2014 and 2015 due to litigation over the charges that the university was not following the J M Lyngdoh Commission's recommendations for student union elections as per the Supreme Court order.
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As many as 16 candidates were in the fray for the post of vice president, and 6 for the post of general secretary.
Results were also announced for the seats of 20 faculty representatives, for which 59 candidates were in fray.
Gujarat Congress president Bharatsinh Solanki said in a statement that BJP's top leaders used "unfair means" to ensure that the NSUI did not win the election, but they failed.
"BJP tried every means to ensure that it does not face defeat, and BJP's top leaders in Vadodara used unfair means to intimidate our candidates, but they were not successful. Police even beat up NSUI candidates yesterday," Solanki claimed.