They supported staying in the UK by 63% to 37%. However, just 2589 students voted out of more than 20,000 eligible to take part.
The poll used the same question which will be put to voters in the referendum next year.
Yes campaigners had said they were confident of victory in the run-up to yesterday's poll.
Both the official campaign bodies, Yes Scotland and Better Together, supported students behind the scenes.
The pro-UK camp played down their chances before the vote.
Carys Hughes, of Glasgow University Better Together, said: "We are really delighted with the win. Our campaign was led by the students and wasn't consumed by party politics.
"The other side seemed to think that having Nicola Sturgeon on the campus for a whole day would win them the day.
"It was because they took the campaign away from the students that they lost."
Yes Scotland chief Blair Jenkins said: "We have to remember some 2500 out of 20,000 students actually cast votes. A large section of the student and general population has yet to make up its mind."
l Two prestigious institutions have announced 10 debates in the run up to the referendum.
The Royal Society of Edinburgh and the British Academy have arranged Enlighten the Constitutional Debate. It will host speakers and discussions involving leading academics.
The first event, Scotland and the EU, will be held on March 13 in Edinburgh.