A scan on Thursday confirmed his worries, as Arsenal try to reel in Chelsea and Manchester United at the top of the league.
Fabregas, who has been in dazzling form for third-placed Arsenal, has scored 19 goals in all competitions this season, and was patched up by Arsenal's medical department this week after receiving a kick against Birmingham City on Saturday.
Given the all-clear to play on Wednesday, Arsenal were run ragged by Barcelona for a solid hour at the Emirates, but he gradually rallied his troops for an unlikely late revival that brought two late goals.
"It was a gamble worth taking," Fabregas said after an epic encounter with his old club, although Wenger may well be questioning his own judgement now, especially with William Gallas and Andrei Arhsavin suffering calf injuries.
Arsenal face Wolverhampton Wanderers at home on Saturday after leaders Manchester United take on second-placed Chelsea at Old Trafford.
With six games remaining Arsenal are four points behind United and three behind Chelsea.
Rooney hurt his ankle in the final minute of Man Utd2-1 loss in Germany [AFP]
Man United on Thursday said that Wayne Rooney sustained only minor ligament damage and did not break a bone in Manchester United's Champions League loss at Bayern Munich on Tuesday.
While Rooney will miss United's match against Chelsea on Saturday, the Premier League leaders haven't given a time-frame for Rooney's return to action.
The England international hurt his ankle in the final minute of Tuesday's 2-1 loss in Germany.
"We're pleased to report that Wayne has not suffered a fracture. The scan revealed only minor ligament damage," United's website said on Thursday.
"For now, the club is not commenting on how many games Wayne is likely to miss."
Manager Alex Ferguson will provide an update at his weekly Friday media conference.
World Cup hopes
The fact there is no fracture should boost Rooney's hopes of being fit for England's World Cup opener against the United States on June 12 in South Africa.
Rooney was England's top scorer during World Cup qualifying with nine goals.
But his injury couldn't have come at a worse time as United chases a record fourth straight Premier League title and a third Champions League final appearance in a row.
Having already scored 34 goals this season, Rooney looked on course to surpass Cristiano Ronaldo's 42-goal haul two seasons ago.
With Michael Owen also out injured, Ferguson is likely to deploy Dimitar Berbatov up front when Chelsea, which is a point behind United in the title race, visit Old Trafford on Saturday.
"Everyone knows how Wayne Rooney is important for this team," Chelsea manager Carlo Ancelotti said.
"He has had a fantastic season but his injury could be an advantage for us."