Pakistan struck with two quick wickets to halt Australia’s early momentum on the opening day of the pink-ball first Test at the Gabba on Thursday.
Openers David Warner and Matt Renshaw looked to have few problems after Australia won the toss, before the tourists hit back late in the first session.
Paceman Mohammad Amir had Warner leg before wicket for 32 after the Australian vice-captain was struck on the pad on leg stump in the 24th over.
Warner was given out by English umpire Ian Gould and did not seek a review, ending an opening stand of 70.
Amir is in the first year of his return to international cricket following a five-year ban over spot-fixing, a scandal which almost ended his burgeoning career.
Khawaja, coming off his man-of-the-match 145 in the day-night third Test in Adelaide against South Africa, lasted just six balls before he was out to a false stroke to leg-spinner Yasir Shah.
Khawaja advanced down the wicket but hit straight into Misbah-ul-Haq’s midriff at short midwicket and was on his way for four.
Shah was introduced into the Pakistan attack after just 10 overs and concentrated on a strategy of bowling at leg stump.
Fiery paceman Wahab Riaz kept a tight rein on the Australians and tested young Renshaw with rising deliveries, but the tall Australian got well behind the ball, showing sound defensive technique.