Said Benrahma scored a penalty after Cristiano Biraghi was adjudged to have handballed in the area following a VAR check.
Benrahma nearly took the net off with his penalty with a fantastic effort to give the Hammers the lead.
But midway through the second half the Italian side hit back through Giacomo Bonaventura's neat finish into the bottom corner of the Hammers net.
It's brought to life a final that had previously been seriously lacking in any kind of quality.
The main talking point of the first half was an unsavoury incident which saw Fiorentina captain Cristiano Biraghi have his head cut open after being struck by objects thrown at him where West Ham fans were sat.
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Despite a tense final being played out, Fiorentina might have believed they were edging the contest.
They started the second-half brightly and West Ham could not get out of their own half.
But one break down the right-hand side saw Bowen get away and he bore down on goal.
However, as he flicked the ball up, Biraghi appeared to push his hand onto the ball and nudge it out of the way.
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The incident was initially missed by the officials before VAR intervened and told the referee to take a second look at the monitor.
And he made the decision to give the penalty, which was duly converted by Benrahma.
But West Ham fans were not celebrating long as five minutes later, Bonaventura squeezed a fine half-volley past Alphonse Areola.