The computer analyst was nominated by a group of students at the University of Glasgow who said they had received Mr Snowden's approval through his lawyer.
The result of the ballot, which opened to students yesterday, was revealed in Glasgow today.
He defeated former champion cyclist Graeme Obree, author Alan Bissett and the Rev Kelvin Holdsworth who also stood.
Mr Snowden became a wanted man when his leaks brought to light secret National Security Agency documents which revealed widespread US surveillance of phone and internet communications.
He is staying in Russia where he was given temporary asylum.
A statement from the group which nominated Mr Snowden said: "We are incredibly delighted to see Edward Snowden elected as the new Rector of Glasgow University.
"We have a proud and virtuous tradition of making significant statements through our rectors and today we have once more championed this idea by proving to the world that we are not apathetic to important issues such as democratic rights.
"Our opposition to pervasive and immoral state intrusion has gone down in the records. What is more, we showed Edward Snowden and other brave whistleblowers that we stand in solidarity with them, regardless of where they are.
"In the following weeks we will continue to campaign for the NSA and GCHQ to cease their assault on our fundamental right to privacy and for Edward Snowden to be recognised as the courageous whistleblower he is, rather than a traitor.
"For now, however, we are simply excited to see what our new rector has to say about the title."