West Ham fans threw empty cups and other items onto the pitch on multiple occasions during the first half, with the most heated incident coming around the half-hour mark when Biraghi went to take a corner.
Biraghi was struck on the head, causing streaks of blood to pour down from the back of his head. He received medical treatment and continued the game with a bandage wrapped around his head.
UEFA urged fans over the in-stadium public address system to stop throwing objects in a message that read: "Attention please! This is an important security announcement. Stop throwing objects on to the pitch immediately! Please respect the players and the officials. Thank you!"
West Ham later issued a statement condemning the actions of a section of the club's supporters.
"West Ham United unreservedly condemn the behaviour of a small number of individuals who threw objects onto the pitch during tonight's UEFA Europa Conference League final," the statement said.
"These actions have no place in football, and do not in any way represent the values of our football club and the overwhelming majority of our supporters, who have behaved impeccably in Prague this week and throughout our last two seasons in European competition. We will work with the Police and other stakeholders to review the incidents and act against anyone found guilty of an offence.
"In line with our zero-tolerance approach, anyone identified will have their details passed to the police and will be given an indefinite ban and therefore be unable to enter London Stadium and travel with the Club. There is no place for this kind of behaviour at West Ham United."
Fans throwing objects has become an increasing issue in European football this season, most notably in the Netherlands where the Dutch Football Association has decided all matches would be stopped immediately if a player or match official was hit by an object from the crowd.