The Poland international damaged his shoulder earlier this term and he aggravated the problem during a warm-up ahead of their match with Manchester City.
Arsene Wenger has confirmed the 25-year-old - who had established himself as Arsenal's first-choice goalkeeper - will head to Germany for surgery.
Wenger explained at a press conference: "We had bad news for Lukasz Fabianski because he needs surgery on his shoulder.
"He has decided after having seen a few specialists that he will have surgery in Germany. It means his season is over."
Manuel Almunia has just returned from an injury lay-off and will now battle with youngster Wojciech Szczesny for the number one jersey.
Wenger continued: "The competition for the places at the moment will be between Wojciech and Almunia. Wojciech will play the next game."
Countryman Szczesny admits he indirectly caused the injury.
He said: "I was warming Fabian up before the game with Manchester City and I took a very powerful shot.
"He made a beautiful save but also got an injury. I didn't do it on purpose, I was just doing my job.
"I feel stupid about it. I even told him it would have been better if he didn't save that shot. I take advantage of my team-mate's misfortunes."
Szczesny has deputised well in Fabianski's absence and prior to the 2-1 win over Everton, had kept three Barclays Premier League clean sheets in a row.
Midfielder Alex Song (thigh) will not feature against Newcastle United on Saturday, but Theo Walcott has recovered from a minor ankle knock picked up in the midweek win over Everton.