Khawaja was struck by a brute of a bouncer from Andre Russell in the second over of Australia's run chase during his side's seven-wicket win in the unofficial practice game at the Nursery Ground on Wednesday.
The left-handed batsman retired hurt and indicated to an area on the right side of his head after the blow and looked in some discomfort as he was escorted off the field by team doctor Richard Saw, reported cricket.com.au.
The 32-year-old, who was then sent to a hospital for scans on his jaw, played no further part in the match and returned to the ground later in the afternoon after being cleared of serious damage.
"It was very scary," said Shaun Marsh, who posted an unbeaten 50 in the victory. "It copped him on the side of the cheekbone The main thing is he is OK and can bounce back pretty quickly," he added.
Earlier, West Indies were bowled out for 229, which Australia chased down with more than 11 overs to spare. Steve Smith starred with the bat as he struck a blistering 76 and shared a 109-run stand with Marsh.
Australia will now take on England and Sri Lanka in their official warm-up matches on May 25 and 27 respectively before beginning their World Cup campaign against Afghanistan on June 1.
( With inputs from IANS )