The decision has been made by UEFA to stop Hammers supporters from travelling abroad, while they have also handed the club a hefty fine.
A section of West Ham fans threw objects and missiles onto the pitch during the final two weeks ago whenever a Fiorentina player went to take a corner in the first.
That included beer cups and electronic cigarettes, which resulted in Fiorentina captain Cristiano Biraghi being struck by one on the top of the head.
It cut his head open, leaving a nasty gash, that gushed blood and had to be taken care of by medical officers.
After West Ham went on to win the competition through a last-minute Jarrod Bowen goal, UEFA announced that they had opened an investigation.
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And the conclusion has come out that the east London outfit will have their fans banned for the first away game of next season's Europa League campaign.
A statement from UEFA read: "The control and disciplinary body decided to ban West Ham United FC from selling tickets to away supporters for its next two Uefa competition matches.
"The second of which being suspended for a probationary period of two years as from the date of this decision, for throwing of objects."
West Ham were also fined £43,000 for the incident, as well as a further £6,900 for a pitch invasion following the full-time whistle in Prague.
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It is not known who the Hammers will play in the Europa League yet - a competition they gained entry to courtesy of winning the Europa Conference League.
The last time they were in the tournament, they reached the semi-finals before losing out to eventual winners Eintracht Frankfurt in 2022.
David Moyes will be hoping to take his side one step further and reach the final, though his own future remains in doubt.
Despite winning the Europa Conference League, there have been question marks over whether or not the Scotsman will continue after battling relegation for much of the campaign.
Michael Carrick has been tipped as a potential successor, who came up through the club's academy and has proved an instant hit at Middlesbrough as a coach.
But Moyes is not the only one who could leave with Declan Rice also looking set to depart.
Arsenal are hot on his tracks as they look to bolster their midfield, but Manchester United and Manchester City are also keen.
However, West Ham are demanding a fee of at least £100million - a figure no club has reached yet.