The club said its directors held an emergency board meeting on Tuesday and the supporter, who it “believes it has identified”, was notified of the decision earlier.
They offered an “unreserved apology to the match official” and said they “deeply regret the national and international attention” the incident had received.
The two sides both play in the Northern Premier League Midlands Division.
“Discriminatory behaviour of any kind will not be tolerated and this incident does not reflect the values of AFC Rushden & Diamonds or the wider non-league football community,” a spokesperson said.
“In a sport where a degree of abuse toward match officials has too often become normalised, we hope that if any positive can be taken from this situation – and the extensive coverage it has received – it is that it has sparked important conversations about how match officials are treated, and what is and is not acceptable.
“We also hope that this incident, and its outcome, serves as a reminder that sexist comments have no place in football.”
On Saturday, Diamonds first team manager Elliot Sandy explained to the club’s media on X, external that the referee stopped the match while the fan was removed from the ground.
At half-time, he said the official told the teams she was uncomfortable continuing the match.
