The card means Alonso will now miss the return leg at Anfield, but Rafa said the tackle did not warrant such a reaction from the referee.
Rafa said: "I have seen the tackle again on television and it was not a yellow card. I am not happy about it and neither is Xabi. It is a pity because it is so clear."
But the boss added that the team will cope without Alonso.
"We played three months without Xabi in the team and we won a lot of games and we will try and do the same," he said.