It has been confirmed the Spain international midfielder will now miss the rest of the season.
Fabregas had passed a fitness test in the warm-up ahead of Wednesday night's quarter-final at the Emirates Stadium, having hardly trained since a hefty challenge from Birmingham's Craig Gardner had left severe bruising to his knee and leg.
Unlucky break: Fabregas is believed to have broken his leg during this challenge with Carles Puyol
Fabregas was involved in a collision with Carles Puyol towards the end of the European tie, which saw the Barcelona captain sent off and the Arsenal skipper smash home the resulting penalty to earn a 2-2 draw
Familiar pose: Fabregas was forced off against Birmingham
Afterwards, though, the Spain midfielder was unable to run properly, leaving the stadium on crutches and fearing the worst.
Arsenal last night confirmed Fabregas had indeed suffered a small crack in his right fibula and would need around six weeks' recovery time.
Wenger stressed there had been no risks taken with Fabregas.
'There were some suggestions that he played with a broken bone - that is not true,' said the Arsenal manager.
'We had two independent doctors with X-rays who clarified the bone was perfectly okay, a bruised bone, but not broken before the [Barcelona] game.
'I am 100 per cent confident and I checked that this morning with our medical team. There is no doubt about that. Medically we were clear.
'Cesc had a test on the morning of the game, he had another test on the warm-up.
'It was in my mind if he had said, 'No I feel pain', I would never force anybody to play.
'I asked him after the warm-up if he felt perfectly all right and he said yes. He had not a broken bone before the game started.'
Wenger claims Arsenal have pinpointed the moment at which Fabregas suffered the break.
He explained: 'We believe that it is from the kick of Puyol on the penalty when he kicks him through the legs.
Off day: Gallas (No 10) lasted 44 minutes against Barcelona
'It is on exactly the place where he got kicked against Birmingham.
'He got the crack on his bone, that means he already had a bruised bone before the game and the kick on it made it split.'
Arsenal also lost both defender William Gallas and forward Andrey Arshavin to injury in the first half against Barcelona.
While Arshavin should be back from a calf problem by the end of the month, the prognosis on Gallas is less positive as he seems unlikely to play again this season.
Gallas, who is out of contract at the end of the current campaign, had been somewhat rushed back from missing eight games with a calf problem.
Problems: Wenger has a long injury list
'It was a gamble which did not pay off and was a mistake, yes,' Wenger admitted. 'Gallas, I would say, is five weeks out.
'He could be back maybe quicker, but I just give myself five weeks because three weeks is a minimum and we will have to be a bit more cautious with him.
'So when we go to the Champions League final, he still has a chance to play.'
The Arsenal manager, however, expects Arshavin to be in contention for the visit of Manchester City on April 24.
The Russia forward, speaking before hearing the results of a scan, feared he had torn his calf, but Wenger had a more positive diagnosis.
'It is a calf strain,' said Wenger, 'so let's count 21 days minimum. Possibly for Manchester City, yes, he should be available for that game.'
Defender Gael Clichy (back) and midfielder Denilson (groin) have, meanwhile, both been passed fit for tomorrow's home game against Wolves when the Gunners will aim to close the gap on Manchester United and Chelsea, who face off at Old Trafford.
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