Shaun Marsh was surprisingly preferred to Khawaja in the team thrashed by 159 runs in Auckland on Wednesday in the first tie of the three-match series.
Australia have also brought in leg-spinner Adam Zampa for the second round in Wellington to replace injured quick James Faulkner.
Khawaja, who has not played an ODI for three years but scored centuries in three consecutive Tests against New Zealand and the West Indies late last year, said Australia have already put the ODI humiliation behind them.
The 29-year-old Pakistan-born left-hander, also downplayed his golden run of form in Tests, saying the ODIs in New Zealand conditions were a new challenge.
"The past is done. I'm feeling really good right now but that doesn't mean I'm going to contribute runs," he said after surveying the wicket at Westpac Stadium.
"New Zealand are very good in their conditions, as we are at home. I think they'll come hard again. They're going to try and win this series 2-0."
New Zealand cricket boss David White described the abusive fans as a minority who were not welcome.
"We don't try and judge the fan behaviour, but we agree there are hard limits and offensive behaviour is one of them," he said.
"A bit of banter, that's fine, but consistent abuse of players is not tolerated."
The Australians, however, denied the crowd behaviour bothered them, with Khawaja saying it was no different to playing an away game in domestic cricket.
"It's not too different. The accents are different and I kind of enjoy that."
The third and final ODI will be played in Hamilton on Monday.
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