Barca were missing stars Lione Messi and Zlatan Ibrahimovic, but still outplayed the visitors.
"The team didn't even go on the pitch and we should reflect on this. On Tuesday our squad was superior to that of the Spaniards," Moratti raged.
"The defeat does not obscure the victories. There isn't any problem with Mourinho. He has my full trust. It has been a useless trip.
"It's something that I would judge as an isolated incident even if it came during an important moment because something like this has never happened before and I believe that it ends here.
"This does not cancel out the good football we have played recently, it doesn't cancel out the continuous progress we have made, nor does it cancel the fact we are having a good season. We have played the worst game at the wrong moment."