Test opener Khawaja appeared immune to the form struggles plaguing those vying to partner him at the top for the Border-Gavaskar trophy, helping the Bulls make headway in reply to NSW's 239.
Wet weather meant only one delivery was bowled across the final two sessions, with Queensland posting 2-96 by the time play was abandoned late on Saturday.
Earlier, Khawaja (58 runs from 129 balls) brought up his second first-class half-century for the summer with the second of his two sixes: a slog over long off from Tanveer Sangha.
Sydney rain paused just long enough for NSW to remove Usman Khawaja — cricket.com.au (@cricketcomau) #SheffieldShield pic.twitter.com/7Z0jOt10RYNovember 2, 2024
But his innings was not without controversy.
NSW's Ryan Hadley thought he'd caught Khawaja at fine leg from Sangha's bowling about an hour into play, only for the veteran to remain at the crease following consultation between the umpires.
Khawaja, on 29 at the time, had earlier survived an LBW shout from Josh Hazlewood's bowling.
Hazlewood and Jack Edwards combined for six consecutive maiden overs to start the day before Matthew Renshaw finally got the Bulls running with a thick edge to the boundary.
But out-of-favour Renshaw failed in his bid to reassert his Test credentials, trapped lbw by Sangha on 25 later in the first session.
The wet conditions meant only one ball was bowled in a delayed second session but it could hardly have been a more crucial one for NSW.
Khawaja edged Edwards to Ollie Davies in the slips as rain continued to fall, with the teams back in the pavilion before another delivery could be bowled.
Angus Lovell (10) and Jack Clayton (0) are due to start at the crease on day three.