Atkinson was already unable to take charge of a fixture on Saturday or Sunday after he and fellow referee Howard Webb were appointed match officials for Monday's play-off between Senegal and Oman to decide the final spot at this summer's Olympics.
Under FIFA rules, referees are not allowed to oversee a game on the eve of a designated travel day for an international fixture - even though the Senegal-Oman match is being played at Coventry's Ricoh Arena.
A referee is allowed to be a fourth official, however, which Atkinson will be at Newcastle's clash with Stoke on Saturday.
That had been determined before Sunday's Wembley controversy, which saw Atkinson award Juan Mata Chelsea's second goal, despite television replays suggesting the midfielder's shot had not crossed the line.
It was the fourth high-profile mistake to have occurred in a game Atkinson has refereed this season and came a week after he and his assistants did not spot a knee-high challenge by Manchester City striker Mario Balotelli or Arsenal's Alex Song.
Atkinson also sparked outrage after sending off Everton's Jack Rodwell in October's Merseyside derby, a red card that was overturned on appeal, and was in charge when the officials failed to notice Clint Hill's header had crossed the line in QPR's defeat at Bolton last month.
Referees chief Mike Riley this week stood down assistant referee Dave Bryan for Tuesday's game between Blackburn and Liverpool following his failure to flag for two offside goals in Chelsea's 2-1 win over Wigan three days earlier.
However, the withdrawal of officials for matches is not necessarily a punishment for poor performances.
It is understood Riley treats each case on its merits, with the decision partly based on whether it is best for an individual to be given another match quickly or to be taken out of the limelight for a short period.