In the opinion of the referee?

[whistleblowerusa]

The answer to your question is clearly stated in the laws (Law 14). When a penalty kick is taken during the normal course of play, or time has been extended at half-time or full time to allow a penalty kick to be taken or retaken, a goal is awarded if, before passing between the goalposts and under the crossbar the ball touches either or both of the goalposts and/or the crossbar, and/or the goalkeeper. If you blew your whistle before the ball entered, this is your common sense working here I think, then play was stopped, the penalty kick was not completed and the kick should be retaken, as well as, the sending off of the offending player.
The call is a good one, but hard to sell. Keep your chin up!