The Canadian student first appeared on the quiz programme in September and has since become a cult personality thanks to his “intense” facial expressions and passionate answers to the questions.
His impressive performances have prompted the hashtag #Monkmania to go viral across social media.
On Monday, viewers took to Twitter to express their disappointment at seeing him lose.
One user said: “Ah, fiddlesticks. But I think we can all agree that the People's Champion is #Monkman.”
Another added: “Monkman will always be a winner in my eyes!”
Monkman will always be a winner in my eyes! #UniversityChallenge— LDayus63 (@lauraday84) April 10, 2017
Another said: "The pressure may have got to Monkman but he's still the real winner to me #universitychallenge."
the pressure may have got to Monkman but he's still the real winner to me #universitychallenge— katie. (@s0nnymoore) April 10, 2017
One viewer said they were "actually wounded that Monkman lost", adding: "He's the hero the world wasn't ready for."
Another described the defeat as "worse than Brexit".
#UniversityChallenge Weirdly, I'm absolutely gutted for Monkman. Took defeat very well too...— Gordon Mc Alester (@gmcalester) April 10, 2017
And another said: "It's all over. Thanks for the memories Monkman - you brilliant, brilliant, BRILLIANT man."
By the end Balliol had won by a comfortable 50 points, 190 points to 140 points.
Professor Stephen Hawking presented the winning quartet of the BBC Two show with the 2017 trophy.
The win for captain Joey Goldman's team ended a losing streak which had seen Oxford colleges lose to their Cambridge counterparts in the final for three years running.
Host Jeremy Paxman congratulated the winners and told Wolfson there was "no shame in being runners-up" and that they had been "one of the most entertaining teams in this year's contest".
For only the second time in the programme's 55-year history, the trophy was presented outside the studio, this time at Cambridge University, where Prof Hawking is based.
There the new champions met the renowned physicist and cosmologist, 75.
He told them: "I have said in the past that it is not clear whether intelligence has any long-term survival value - bacteria multiply and flourish without it.
"But it is one of the most admirable qualities, especially when displayed by such young minds.
"Many congratulations to both teams but especially to Balliol College Oxford on becoming series champions on University Challenge, a programme I have long enjoyed."