Referee Graham Poll walked from the Goodison Park pitch with the home fans howling "cheat" at the World Cup official as Arsenal booked their place in the Carling Cup quarter-finals.
Poll enraged Everton supporters for sending off James McFadden for dissent after just 18 minutes of the tie, which was settled by Emmanuel Adebayor's 85th-minute header.
Television replays seemed to suggest that Poll was telling Everton players that McFadden had called him a cheat, even though the Scottish forward is understood to have denied that accusation to his team-mates in the dressing room.
But with Poll involved in controversy already following his handling of Chelsea's defeat at Tottenham and his dismissal of John Terry, the locals were not going to give him an inch.
Arsene Wenger made a remarkable 11 changes from the side which lost at West Ham in such dramatic fashion on Sunday.
All five of the Arsenal substitutes at Upton Park started this fourth-round tie, with Theo Walcott also on from the start.
Everton left out Simon Davies and Alan Stubbs from the side that lost at Fulham, bringing in McFadden and Nuno Valente for a match that was David Moyes' 200th as Blues boss.
Arsenal's second string had Everton chasing shadows in the opening minutes with possession, movement and passing.
Everton favoured a more direct approach and Leon Osman's cross was pulled down by McFadden, but Armand Traore hacked the ball clear.
Alexandre Song was then booked in the 15th minute for a foul on Mikel Arteta, his third offence of the game.
But Poll was then thrust into the spotlight when Andrew Johnson fell in the box under pressure from three defenders, with Philippe Senderos looking to have committed the foul.
Poll waved away penalty appeals and Goodison Park erupted in anger. McFadden clearly said far too much for Poll's liking as he raced past the referee, who instantly produced a red card and Everton were down to 10 men.
Poll was getting plenty of abuse now from the Goodison fans, who were quick to remind him he had "messed up" at the World Cup.
Everton's response was equally fierce. They were still able to power forward, and Joseph Yobo headed agonisingly wide from an Arteta corner on 27 minutes.
Ten minutes later Jeremie Aliadiere was booked for hauling down Arteta, and from the free-kick Johnson set up Arteta for a curling effort that Manuel Almunia pushed away.
Arsenal sent on goalkeeper Mart Poom at the break for Almunia, the Spaniard still suffering from the kick he received early in the game as Traore cleared under pressure from McFadden.
At times Johnson was the only Everton player not employed on the edge of their box, surrounded by four defenders. But he kept battling away and on 50 minutes turned 20 yards out to force a fine save from Poom with a hooked volley.
But it was hard graft for Everton now, as they withstood an almost constant flow of pressure towards them, Mathieu Flamini and the excellent Denilson pulling the strings.
Adebayor was next into the book, the latest to send Arteta spinning, before a thunderous tackle by Valente on Denilson sent the Brazilian hurtling into the air, but Poll did not penalise the challenge.
Aliadiere then went on a high-speed 40-yard run that ended with him flat on his face in the box after a Joleon Lescott challenge, and Poll waved that one away too.
Denilson had come back onto the pitch, but a couple of minutes later collapsed again and was led away after treatment, Mark Randall taking over on 69 minutes.
Despite plenty of possession, Arsenal were creating few chances and it took another surging run from Johnson - who tumbled under a challenge from Johan Djourou - to get the crowd roaring. Wenger reacted to that one, laughing and waving his arm at what he considered another attempt to influence Poll.
Everton were under constant pressure by now, and Arsenal finally got the ball into the net with five minutes to go, Adebayor hurling himself into the box to head home a Flamini corner.
Everton threw on striker Victor Anichebe for Lee Carsley in injury time, but could not rescue their cup dreams.
Teams:
Everton (0) 0 Arsenal (0) 1
Everton Howard, Neville, Yobo, Lescott, Nuno Valente, Osman,Cahill, Carsley (Anichebe 90), Arteta, Johnson, McFadden.
Subs Not Used: Turner, Weir, Davies, Stubbs.
Sent Off: McFadden (19).
Arsenal Almunia (Poom 46), Eboue, Senderos, Djourou, Flamini,Walcott, Song Billong, Denilson (Randall 70), Adebayor, Traore,Aliadiere.
Subs Not Used: Connolly, Ryan Garry, Perez.
Booked: Song Billong, Aliadiere, Adebayor.
Goals: Adebayor 85.
Att: 31,045
Ref: G Poll (Hertfordshire).
