It is the second European trophy for West Ham after they won the now defunct Cup Winners’ Cup 58 years ago with a team including England World Cup heroes Bobby Moore and Geoff Hurst.
Bowen picked up a superb through ball from Lucas Paqueta, before sending a low shot past a helpless Pietro Terracciano in the Fiorentina goal.
“I obviously dreamed of scoring but to score the winner in the last minute. It’s what you always say you want to do,” Bowen told BT Sport.
“To do it in front of these fans. I thought I was going to cry. I’m just happy.”
Said Benrahma had opened the scoring for West Ham in Prague as he blasted a penalty past Terracciano on 62 minutes after VAR had caught Cristiano Biraghi handling the ball trying to stop Bowen in the box.
Giacomo Bonaventura levelled five minutes later, beating West Ham goalkeeper Alphonse Areola with a fine, low right-footed effort.
Bonaventura capitalised on a superb header back from Nicolas Gonzalez who had leapt over West Ham full-back Emerson.
The champions’ name will be the second ever on the Conference League trophy following Roma, who won the maiden edition of the competition last year.
West Ham have also clinched a spot in next season’s Europa League with the win, while Fiorentina will miss out on European competition after finishing eighth in the Serie A.
West Ham’s previous major trophy was back in 1980 when they won the FA Cup.
They spent most of the last season battling the prospect of relegation, finishing 14th in the Premier League in the end.
‘Over the moon’
“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,” Bowen said.
“This is the biggest game of my career. The emotion, there was time for one more chance. I’m just so happy.”
The game got off to a slow start, although Michail Antonio tested Terracciano with a low shot on 40 seconds.
Fiorentina dominated possession and looked more organised in a largely uneventful first half.
But they did not came close until injury time when Christian Kouame headed against the post from Gonzalez’s cross.
Fiorentina striker Luka Jovic then tapped the ball across the line on a rebound but his goal was ruled out for offside.
Declan Rice’s 13th-minute shot from outside the box whizzed just past the post in the Hammers’ best chance of the first half.
Rice may have played his last game for the East Londoners as he is being courted by the likes of Arsenal, Chelsea and Manchester United.
The game changed with the goals as both sides suddenly looked far more lively, earning corners and creating chances.
But Rolando Mandragora sent his shot just wide and Sofyan Amrabat was denied by Areola, while Tomas Soucek’s header was saved by a diving Terracciano.
Before the game, Prague police said they had detained 16 people as Fiorentina fans attacked West Ham supporters in a bar in central Prague. Three people sustained light injuries.
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