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."
BEAUTIFUL SAVE
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.