Despite his rich vein of form, the 29-year-old top order batsman was still omitted from the original Australia squad for the three-match ODI series in New Zealand before a hamstring injury to Aaron Finch led to his recall.
The team management, however, opted to persist with Shaun Marsh, rewarding him for two fifties in the three ODIs he played against India last month.
"He's unlucky to miss out but Shaun's going to get the first opportunity," Smith said at Auckland on Tuesday.
"No doubt he'd be frustrated. He's hitting the ball extremely well."
The Australian captain said it was very difficult to break into a well-set team that had been performing really well but suggested Khawaja would get a chance in one of the two remaining matches that precede a two-test series between the teams.
Khawaja was selected in the test squad for those matches.
"We're the current world champions. We've been playing some very good one-day cricket and the batters have been scoring lots of runs," Smith added.
"We scored 300 on every occasion in the recent one-day series (against India) at home."
"I think he'll play one of the (three ODI) games at least," the skipper said.
"He does need a hit going into what is a big test series and he's batting extremely well. I'm sure if he gets an opportunity, he'll take it with both hands."
(Reporting by Amlan Chakraborty in New Delhi; Editing by John O'Brien)
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