The 28-year-old lefthander, who returned from more than two years in the test wilderness to score centuries in the first two matches against the Black Caps, pulled up while chasing a ball to the boundary.
Cricket Australia on Sunday confirmed the Pakistan-born batsman would miss the final match of the New Zealand series and the opening test against West Indies.
"Usman suffered a left hamstring injury in the field yesterday afternoon and underwent scans in Perth this morning," team physiotherapist David Beakley said in a news release.
"The scans have indicated a moderate hamstring muscle strain which means it is likely he will be unavailable for the next two test matches in Adelaide and Hobart."
Australia meet New Zealand in the world's first day-night test match starting on Nov. 27 at the Adelaide Oval and play the first of their three matches against West Indies in Tasmania in mid December.
Khawaja missed much of last summer with a left knee injury and his absence from the side will be a big blow to Australia, who have often struggled to fill the number three berth in the batting order.
His new setback may pave the way for a test call-up for one of the Western Australian duo of Shaun Marsh or Cameron Bancroft.
(Reporting by Nick Mulvenney in Sydney, editing by Patrick Johnston)
