Dave Bryan has been removed from running the line in Tuesday's game between Blackburn and Liverpool following a decision by the Professional Game Match Officials, who agree appointments with the Premier League.
Bryan neglected to flag for offside for Chelsea's opening goal despite Branislav Ivanovic standing well offside, and the assistant referee compounded his mistake when he failed to spot Juan Mata marginally offside for the Blues' stoppage-time winner.
Wigan manager Roberto Martinez described the decisions as "horrific" and "disgusting".
Martinez is now waiting to learn whether he will face a Football Association charge for his outspoken attack.
The withdrawal of officials for matches is not necessarily a punishment for poor performances.
It is understood referees' chief Mike Riley treats each case on its merits, with the decision partly based on whether it is best for an official to been given another match quickly or to be taken out of the limelight for a short period.
Elsewhere in the Premier League QPR boss Mark Hughes has confirmed the club will appeal against Shaun Derry's red card during Sunday's 2-0 defeat to Manchester United.
Derry was sent off for denying Ashley Young a clear goalscoring opportunity, but TV replays showed the decision was debatable and the United winger had been offside anyway.
The midfielder is set to miss Wednesday's encounter with Swansea at Loftus Road, but Hughes will challenge the dismissal.
"Yes. We will appeal the red card," said Hughes.
"We need all hands on deck on Wednesday, plus Shaun has had a rest. He only played for 15 minutes."