One man from Halifax was arrested during crowd trouble at the Chester City v FC Halifax Town match.
A Cheshire police spokesman said there was chanting between rival fans in the city centre ahead of the third qualifying round clash but no reports of trouble.
But, three fans were later evicted from the ground after invading the pitch and it was then the arrest was made for a public order offence.
What was a gripping cup-tie was marred by unruly fans.
Less than two minutes into the match a small band of fans from the Halifax contingent burst onto the pitch to confront Chester supporters in the Harry McNally Terrace.
Punches were thrown and further trouble erupted in the 22nd minute in the corner of the East Stand and stewards tried to stop the ill-feeling spilling over further.
FC Halifax manager Neil Aspin said the referee was right to continue with the game.
“It didn’t go on for too long. You could see the players were focussed on the game and not on the crowd trouble,” he said.
“You don’t want to give them a platform where they think they’ve disrupted the game so I think he did well to continue.
“It’s not something I want to see at football matches and anything that takes away from the good name of the club is not something I want to see.”
Chester Manager Neil Young said: “It’s disappointing. I saw Halifax fans jumping over trying to goad Chester fans and you don’t need that in football.”
Pat Cluskey, chief executive of Chester FC said his club’s decision to give the entire West Stand to FC Halifax Town fans - around 500 travelled - was justified in light of the crowd trouble.
“I spoke to the police and they are delighted with the way the Chester stewards dealt with the issue.
“Halifax did write to us in the last week to advise us that they have a potential unruly element following them at the moment so both Halifax and Chester have been proactive.
“I’m pleased that the stewards dealt with the issue as well as they did.”
The match, during which each team had a man sent off, ended 1-1 and the replay will be at the Shay on Tuesday night.
Mr Cluskey said he hoped the security for the replay would be as good at the Shay.