The Gunners captain had been a doubt for the game which ended in a dramatic 2-2 draw at Emirates Stadium, after suffering severe bruising to his knee and leg at Birmingham.
However, after coming through a fitness test in the warm-up, Fabregas returned to lead the side against his boyhood club - and played a pivotal role in their comeback after falling 2-0 down to a brace from Zlatan Ibrahimovic which looked to have all but killed off the tie.
Floored: Arsenal players show their concern as injured Fabregas goes down
During the closing stages, after substitute Theo Walcott had pulleda goal back, the Gunners skipper - who would have missed the second legagainst his old club anyway after being booked in the first half - wasbundled over by Carles Puyol and awarded a penalty.
It was during that collision with the Barcelona captain, who wasshown a red card by Swiss referee Massimo Busacca, that Fabregassuffered the latest problem.
However, while Fabregas will miss the rest of the domestic season,the 22-year-old should still be fit for the World Cup with Spain although huge question marks will hang over his match fitness.
An Arsenal statement read: 'Following a scan this afternoon, theclub can confirm that Cesc Fabregas has suffered a small crack in hisright fibula as a result of the collision with Barcelona defenderCarles Puyol during Wednesday evening's match.
'As a consequence, Cesc will miss the remainder of the domestic campaign as he will be out of action for at six weeks.
'Everyone at the club wishes Cesc a full and speedy recovery.'
No mistake: Fabregas held his nerve to bullet home his penalty
Fabregas left Emirates Stadium on crutches last night, and had admitted he feared the worst.
The news will be a devastating blow to the plans of manager Arsene Wenger, who had only just got his captain back into full action after a hamstring injury earlier in the campaign.
Wenger will also have to do without Russian playmaker Andrey Arshavin for up to three weeks after he picked up a calf problem against Barcelona and had to be substituted.
Defender William Gallas, meanwhile, also looks set to be unavailable for the remainder of the campaign after he broke down on his return following eight games out with a calf injury.
On the mend: Van Persie
Arsenal resume their Barclays Premier League title race with the visit of Wolves on Saturday.
With leaders Manchester United hosting Chelsea, the Gunners could close the current gap, which stands at four points, with victory over Mick McCarthy's relegation battlers - who have won two of their last four games to pull clear of the drop zone.
Wenger, meanwhile, hopes Holland forward Robin van Persie could be back in action by the end of the month after suffering what turned out to be a serious ankle injury while on international duty during November.
The Arsenal manager said: 'The latest news on Robin van Persie is very promising, but we have to wait two more weeks to integrate him fully into first team training. Let's hope we can give him some big games to aim for at the end of the season.'
Gunners winger Walcott knows there is no further margin for error against Wolves in the wake of last weekend's draw at Birmingham, where Arsenal conceded a stoppage-time equaliser.
'Every single game is a cup tie especially with the league title race,' the England forward said. 'We need to clock up some points and add to our goal difference to show we are still in the race.'
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