James Beattie was dropped to the Everton bench as youngster James Vaughan was brought in to partner Andy Johnson.
The partnership instantly jelled as David Moyes' side took the game to Arsenal. Johnson, Mikel Arteta and Manuel Fernandes linked well to give the Gunners defence a hint of the afternoon that was in store for them.
The Arsenal midfield found it difficult to get a foothold in the game as they conceded possession time and again during the opening exchanges.
Jens Lehmann did fantastically well to keep Johnson out on ten minutes as the striker beat the keeper to the ball in his own area. The German star reached around the back of the former Crystal Palace hit-man to scoop the ball out of play.
The Everton fans sensed an upset as the excellent Fernandes and Arteta created space for their strikers to exploit, although a clear sight of goal was proving elusive.
In the first 20 minutes Tomas Rosicky and co resorted to firing shots in from long range.
Lee Carsley hit the Arsenal post with a 25-yard screamer on 26 minutes as the Toffees went in search of the goal their play merited.
Fredrik Ljungberg and Cesc Fabregas were having indifferent games with Julio Baptista almost anonymous.
Jeremie Aliadiere forced a save from Tim Howard on 38 minutes which sparked a five-minute Arsenal revival as they peppered the Everton goal with shots and free-kicks.
Everton began the second half in the ascendancy yet again. Fernandes should have done better when free on the right of Lehmann's goal but shot wide after good work by Johnson. Joseph Yobo and Arteta both also went close.
Arsenal began to look a little more cohesive as the half progressed and could have scored after a horrendous back-pass by Joleon Lescott which Howard just managed to reach.
Everton hit the post yet again through Leon Osman as the game really got going.
Howard spilled a Fabregas 30-yarder to fray Evertonian nerves on 79 minutes and it was the hosts that turned the screw as the game drew to a close.
Johnson cemented his place as the latest Goodison hero when he made no mistake from six yards out in stoppage time as he gleefully buried the ball into the Arsenal net to give extra zip to Everton's European assault.