Darren Drysdale will not referee his scheduled match this weekend following his altercation with Ipswich's Alan Judge on Tuesday.
Drysdale, an RAF sergeant from Lincolnshire, was charged with improper conduct by the FA after squaring up to Judge in the latter stages of Ipswich's game against Northampton.
After apologising on Wednesday, the PGMOL have now taken Drysdale - who turned 50 today - off the League One clash between Southend and Bolton on Saturday, replacing him with Declan Bourne.
In his statement via the PGMOL, Drysdale admitted he had done wrong and apologised to Judge and Ipswich Town.
'I fully understand that it is important to maintain our composure throughout the game and always engage with players in a professional manner,' he said.
'I'm sorry that I did not do that last night and I can only apologise to Alan and Ipswich Town.'
Ipswich midfielder Judge, meanwhile, insisted he was not looking for an apology from Drysdale nor pressing an FA Charge, saying: 'Referees have a tough job to do and it was heat of the moment stuff that happens in football.
'The photo makes it look worse than it was and to be honest, the matter was finished with from my end as soon as I walked off the pitch.
'I wasn't looking for the referee to apologise; I wasn't looking for him to be charged. There was never going to be a complaint from me and I made that clear.
'Like I said, for me - it was finished with straight away.'
But an FA statement on Wednesday evening said: 'Darren Drysdale has been charged with a breach of FA Rule E3 following Tuesday night's EFL League One game between Ipswich Town FC and Northampton Town FC.
'It is alleged that the match official's behaviour during the 90th minute of the game amounts to improper conduct and he has until Thursday 4 March 2021 to provide a response.'
Sportsmail columnist and former Premier League referee Mark Clattenburg said of the incident: ‘All referees, even when abused, need to keep self discipline. They must show restraint and maintain professionalism.’
The referee has however received support from a number of players on social media, including Aston Villa's England internationals Jack Grealish and Tyrone Mings.
Grealish wrote: 'Ah come on?! No need to apologise at all! I think it's brilliant.'
And his team-mate Mings believes more needs to be done to ensure referees receive respect from players.
'Refs and officials put up with a lot from players. I'm sure he isn't proud of it but in the world we're living in, I think you can allow for some compassion when people don't always act as they should,' Mings replied to a tweet.