Everton drew 1-1 for a 5-1 aggregate victory after a match which saw full-back Hibbert sent off in just the seventh minute for bringing down Jakub Petr.
Steven Pienaar scored shortly before half-time - and despite substitute Pavel Sultes' equaliser for the Czechs, David Moyes' men were in control.
"It was a job well done," the Toffees boss told evertonTV.
"I am pleased we got through - it was important for us. I thought we got better as the game went on.
"They put us under pressure, but thankfully we defended well enough and got one ourselves."
Replays suggested Hibbert might have got the ball when he was judged to have committed the foul - and also that more defenders might have been covering to prevent Petr getting a shot on goal.
"It was disappointing to see Tony get sent off, and that affected us," Moyes added.
"I thought it was a wee bit harsh; I have seen them given (in similar situations) and seen them not.
"But in Europe, if you mis-place passes you will put your defenders in trouble - and you will probably end up making rash tackles, which will be punished."