West Ham promised to issue lifetime bans to unruly fans after Manchester United's team bus was attacked by supporters prior to kick-off.
Wednesday's (AEST) stunning 3-2 Premier League victory and farewell to Upton Park was overshadowed as West Ham fans pelted United's coach with bottles on their approach to the ground.
The pre-game scenes and United's late arrival forced kick-off to be delayed by 45 minutes.
West Ham is working with police to as they attempt to identify those involved in the attack.
"It was an extraordinary night full of extraordinary moments in front of extraordinary fans. 99 per cent of whom behaved impeccably and were a credit to the club," the club's statement read.
"We have already had thousands of tweets and emails from fans to say how proud they were to be a part of such a special evening in West Ham's history.
"However, we are aware that there were some supporters outside the Boleyn Ground who didn't act in an appropriate way when the Manchester United team bus was damaged.
"That was not acceptable and we will work with the police to identify those responsible and ban them for life."
Winston Reid was the hero for sixth-placed West Ham, which played its final game at Upton Park before making the move to the Olympic Stadium next season.
Reid netted the 80th-minute winner after Michail Antonio had equalised four minutes earlier, cancelling out a second-half brace from United star Anthony Martial.
Diafra Sakho had opened the scoring for West Ham 10 minutes into the game.