From row two, Alonso made a good start to challenge leader Sebastian Vettel, but he got too close to the Red Bull and nudged its rear at Turn 2.
Alonso continued in second, under attack from Mark Webber, until the front wing folded under the car approaching the first corner on lap two.
The Ferrari went off and Alonso was unable to get the F138 out of the gravel. The team had hoped he could continue until it was time to pit for dry tyres.
"We took a risk that didn't pay off," admitted Domenicali.
"After the touch, the race was not over and I considered the situation where there was a transition from wet to dry.
"In normal conditions you would come in, but in this transition, if you believe the wing can survive, you try and bide your time. You may have the chance to pit to change to the dry tyres and be the hero of the weekend.
"Unfortunately the wing didn't stay there."
Domenicali underlined it had been the team's decision to take the risk, not Alonso's.
"The decision was from the pitwall," he added. "Obviously Fernando can feel it in the car, but he could not see the damage from his view.
"We take the responsibility as the team. The 'kiss' [on Vettel's car] was unfortunate because we could have taken good points from this race.
"Fernando's not happy to come away with zero points, but he's positive and looking forward because he knows we have something to play with."
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