Three men were arrested during violent clashes between rival fans hours before Albion's FA Cup match at Aldershot.
Fighting broke out in a town centre pub two hours before kick-off in the first-round game.
The violence spilled over into the streets and into two other pubs after the brawl erupted at Shooters Bar.
All three pubs closed for the rest of the afternoon after supporters threw tables and chairs through windows before causing trouble at the other bars.
Witnesses saw one Aldershot supporter being hit over the head with an ashtray and repeatedly kicked after a group of Albion fans burst into the Beehive pub in the town's High Street.
The trouble marred an otherwise happy day for the vast majority of Albion fans who behaved impeccably and cheered their team on to a 6-2 win.
More than 2,200 Albion fans made the trip to watch the Seagulls win against Ryman League Aldershot, taking the team into the second round of the competition.
Catherine Thorpe, landlady of the Beehive Pub, said: "We had a marvellous time with supporters from both sides but after the trouble in Shooters - I presume it must have been the same set - they just barged in through the doors.
"I find it a bit insulting. I had loads of Albion fans in here and they were all great, mixing with the fans from Aldershot.
"But then this one group came in. There is just a set that are out to cause trouble.
"Most of the Brighton supporters actually apologised on their way out. I think they were just as upset about it as we were.
"It was over very quickly and at that point everybody was asked to leave."
Mrs Thorpe closed her pub's doors for the rest of the day and kept the lights switched off in case any hooligans returned.
Inspector Paul Martin, of Hampshire police, said a small group of Albion fans were largely to blame for the trouble but said fans of both teams joined in.
Albion chief executive Martin Perry said: "There was a small minority, yet again, who have caused trouble.
"If we get any details which will allow us to take action, they will be banned."
Dean Chapman, 33, of Langley Crescent, Brighton, was charged with affray and is due before Aldershot magistrates on Thursday.
A 32-year-old Hove man was arrested for criminal damage but was later released on police bail and a 34-year-old Aldershot fan was arrested and cautioned for a public order offence during the match.
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