Dr Arthur Bernhoff seen off US Office actor Brian Baumgartner - who finished second - and Scottish Green MSP Q Manivannan, who came third.
Bernhoff, a St Andrews graduate who lives locally, has pledged to be a "present, listening, and effective" rector, and will take up his post on 1 November.
A new rector is elected every three years to represent the interests of students on the university court.
Turnout was just under 45% - almost double the turnout of the last rector election in 2023, and the biggest response to a rector's election in recent history.
In the fourth round of voting, Dr Bernhoff secured 3,135 votes, and actor Brian Baumgartner, known for playing Kevin Malone in the US version of The Office, came second with 1,553 votes.
Scottish Greens MSP Dr Q Manivannan came third with 1,243 votes and was eliminated in the third round.
Manivannan identifies as non-binary and uses they/them pronouns, and is one of the first two openly trans MSPs at Holyrood, alongside fellow Green Iris Duane.
Earlier this week, Monty Python actor John Cleese urged students not to vote for Manivannan due to the politician's controversial comments about rape.
In a podcast last year, Manivannan spoke about the "demonisation of rape", adding that the crime existed on a "spectrum".
Cleese, a former rector at St Andrews, accused the MSP of trying to "understate the appalling psychological effects of rape".
Manivannan apologised earlier this year for any hurt caused, but said the comments had been "maliciously" edited.
Their remarks about rape were reported following May's Scottish Parliament election.
Appearing on The Subjective Space podcast, Manivannan spoke of the "demonisation of rape", and said: "It is a spectrum – none of which is any worse or less or more worse."
Their comments were criticised by the Scottish Rape Crisis Alliance, which accused the MSP of trying to "minimise" sexual violence.
Apologising for the comments, they said: "I am horrified that my comments were selectively edited in order to mislead people and misrepresent me.
"But I also accept that my language was abstract in the first place and for that I take full responsibility and am sorry."
Dr Bernhoff holds an analytical role with the Ministry of Defence and remains a Foreign, Commonwealth & Development Office (FCDO) deployable civilian expert.
He will be formally installed at a ceremony in 2027 and take part in the traditional student "drag" around the Fife town as part of the celebrations.
Dr Bernhoff said: "I am honoured and humbled by the level of support that I received during the campaign and the election from all the different parts of the student body.
"Over the past few weeks, and particularly in the last few days, students have very generously talked to me about their experiences, and shared their perspectives.
"As a proud alumni, it has been a great pleasure and a privilege to reconnect with the university where I have spent some of the most formative years of my life."
He said he hoped to make the university "even stronger, where students from all backgrounds, and of all characteristics can thrive and build strong foundations for lives beyond their time in higher education."
Previous rectors at the University of St Andrews have included authors JM Barrie and Rudyard Kipling.
Bernhoff will become the 56th person to hold the post.