Fabregas, who left the Arsenal stadium on crutches following a 2-2 draw, said he would undergo a scan on Thursday to ascertain the extent of the injury.
"I'm not good. I fear the worst, which is that I have broken something," Fabregas told reporters.
"We have to wait until tomorrow but I hope I can play in an Arsenal shirt again this season.
"I fear it won't be good news but I still hope it will be."
Fabregas, who can expect to be in the Spain squad for the World Cup in South Africa if fit, went down in obvious pain after scoring the penalty equaliser against Barcelona in the first leg.
He had been a doubt going into the game after injuring his knee against Birmingham in the Premier League on Saturday.
Arsenal paid a heavy price for their comeback draw on Wednesday, with French international William Gallas suffering a calf injury that could mean he does not play again before the World Cup.
"He pulled his calf muscle and I think it's the end of the season for him," Arsenal manager Wenger told French TV channel Canal Plus.
"I do not include the World Cup. I think he will be ready for the World Cup," added Wenger, speaking of the tournament to be held in South Africa from June 11-July 11.
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