Wenger - Fabregas was fit to play
It was confirmed on Friday that the Spain international midfielder will now miss the rest of the season after suffering a small crack in his right fibula.
But Wenger stressed no risks had been taken with Fabregas and said: "There were some suggestions that he played with a broken bone - that is not true."
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.
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
Afterwards, though, the Spain midfielder was unable to run properly and he is now set to be sidelined for the remainder of the campaign.
Wenger added: "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% confident and I checked that 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. 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."
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