The tourists were 138 for no loss at the lunch break, still 338 behind but they scored at 4.18 runs per over, which is significantly better than Pakistan’s under-three run rate.
Islamabad-born Khawaja was batting on 70 at the break, while Warner was on 60 with the openers having hit a combined 23 boundaries.
Earlier after Australia resumed on five for no loss, Warner looked in discomfort against Shaheen Afridi at the Pindi Cricket Stadium.
At the other end, Khawaja was fluent though he could have been dismissed on 22.
Afridi got the opener to drive away from his body but Fawad Alam spilled a straight-forward catch at gully.
It was a costly mistake on a flat track where bowlers have struggled for success and only four wickets fell in the first two days.
The session also witnessed a little duel between Warner and Naseem Shah.
Warner hit the pacer for two boundaries in an over and Naseem responded by bowling into the opener’s body in his next over.
Warner suffered a blow on his upper arm but laughed it off when Naseem gave him a stare and a piece of his mind.
Khawaja played a spectacular upper-cut against Naseem and then took two runs off spinner Sajid Khan to bring up a breezy half-century.
Warner welcomed off-spinner Iftikhar Ahmed into the attack by hitting him for three boundaries the first of which brought up his fifty.