Let's not forget that the morning session is 2.5 hours long. No reason why Australia couldn't bat for 1.5-2 hours. Get a 150-200 run lead and give the quicks a burst before lunch and then keep the pressure up for the rest of the day. With Duminy out of the match SA will be heavily reliant on their top order.
Lyon was also hardly terrible bowling in the first innings. With a few foot marks to go with the bounce he was getting previously he could cause some trouble.