Not long after the Czechs were awarded a questionable penalty, which was converted to make it 2-2, Hubnik challenged the Wolves defender in the Scotland area but did not touch the ball in his pursuit to halt the forward advance.
Berra went down under the injury-time challenge but referee Kevin Blom, first booked Berrs for diving, then waved away the Scottish protests and the game ended in a draw, making life difficult for Craig Levein's men who are now five points behind the second-placed Czechs when a more positive result would have had them trailing by one.
And to make matters worse, Hertha Berlin's Hubnik said he did make contact with Berra but said it was similar to an earlier incident which went unpunished for the Czech side.
"There was contact with the Scotland player. But it's up to the referee," Hubnik said.
"It was the same for us with Milan Baros in the first half. The referee also decided that was not a penalty.
"I was tired when I made my challenge to the Scotland player. It was in the last minute and it had been a hard game.
"I looked straightaway at the ref - and I was relieved with his decision.
"I believe the player made good contact with me and he helped make the referee feel it was not 100 per cent.
"It was a very difficult split-second for me.
"I reacted by making it clear I felt it wasn't a penalty. But this is normal for any player with the score at that stage."