Khawaja was struck by a bouncer from Andre Russell in the second over while Australia was chasing 230, forcing the opener to retire hurt.
He looked in discomfort and walked off the field accompanied by Australian team doctor Richard Saw, sending a scare through the Australian World Cup camp.
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However, scans on his jaw later cleared him of any serious injury as Australia breathed a sigh of relief.
“It was very scary. It copped him on the side of the cheekbone—The main thing is he is OK and can bounce back pretty quickly. (Khawaja was) a bit shaken, as you are when you get hit on the head. But he is a tough cookie, Uzzy, and he'll be ready to go,” said Shaun Marsh, who hit an unbeaten half-century in the victory.
Khawaja didn't take part in the match again even as Australia went on to register a seven-wicket victory over West Indies in the first of their three warm-up games. He is expected to be available for selection for Australia's next warm-up match against England on Saturday.