The Frenchman returned to action in the first leg of United's Europa League last-16 tie with Russian side Anzhi Makhachkala after 12 weeks out.
But Ben Arfa lasted only 64 minutes of that game and missed the second leg clash at St James' Park on Thursday night, where Newcastle progressed to face Benfica in the quarter-finals after a last-gasp Papiss Cisse goal gave them a 1-0 win over Anzhi.
Ben Arfa is not expected back until pre-season training for the 2013/14 campaign, with Newcastle manager Alan Pardew confirming he will not be rushed back sooner, even if they qualify for the Europa League final.
"It's a shame for Hatem because we went down this process of not operating on it, and I think now that's an option that we might need to take," said Pardew.
"But we can't now put him at risk. Even if it was to get to a Europa League final, I don't think that's going to be the case.
"We need to look to next year for him and just go forward together knowing we haven't got him on board."
Pardew admitted they miss the quality he offers but insists they have a strong enough squad to cope without him.
"He gives us that X-factor. In a game like last night's where he could open the door for us, we haven't got that luxury," added Pardew.
"Unfortunately for Hatem, that's the news that he didn't want to hear.
"But as far as we are concerned, the team has responded well in his absence and hopefully, we do that until the end of the year."
You can only watch the best Premier League coverage here on Sky Sports. Watch Wigan Athletic v Newcastle United exclusively live on Sky Sports 1HD, 3D and Sky Go from 3.30pm on Sunday 17th March. Click here for more details