The Hammers edged out their Italian opponents 2-1 in Prague to win their first trophy since 1980.
Incredibly, Bowen is the first Englishman to score a winner in a European final since Alan Smith for Arsenal in the 1994 European Cup Winners' Cup.
David Moyes' side took the lead just after the hour mark through Said Benrahma's penalty.
But Fiorentina equalised almost immediately after thanks to Giacomo Bonaventura's smart volley.
And just when the game looked to be heading into extra-time, Bowen latched onto a Lucas Paqueta through ball to calmly slot the ball home.
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It sparked wild celebrations from the players and fans as Moyes channelled his inner-Jose Mourinho to sprint down the touchline.
Fiorentina pressed in search of a late strike, but it was to no avail as the Hammers finally ended 43 years of hurt.
There were ugly scenes in the first half when Fiorentina skipper Cristiano Biraghi was hit on the head by an object from a West Ham that caused him to bleed.
Cups and vape pens were thrown on the pitch, which saw Hammers skipper Declan Rice - in his potential last match for the club - try to calm down the travelling supporters.
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Tempers calmed down in the second half, as both teams looked to get a foothold in the match.
Speaking to BT Sport after his goal, Bowen said: "I obviously dreamed of scoring but to score the winner in the last minute.
"It's what you always say you want to do. To do it in front of these fans. I thought I was going to cry. I'm just happy.
"We had a dream, we haven't had the best season, myself included, but to give these fans this moment, I'm over the moon.
"I think in my position you make that run 10 times you might get that ball once. As soon as you get it you've got to put it away.
"Never [have I felt like this in my life]. This is the biggest game of my career. The emotion, there was time for one more chance. I'm just so happy. I'm over the moon.
"I'm thinking of the party tonight. Listen to it. Listen."
More will follow.
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