The 35-year-old suffered a groin adductor injury in Wellington Phoenix's 3-2 loss to Sydney FC in the A-League last Sunday. Scans on Thursday confirmed the extent of the injury, local media reported, which would keep him out of action for up to 12 weeks.
The Oceania champions face Peru, who finished fifth in South American qualifying, in the first leg of the intercontinental playoff in Wellington on Nov. 11 before heading to Lima for the second leg on Nov. 15.
Durante played alongside captain Winston Reid and Michael Boxall in defence in the All Whites' last match, a 2-1 loss to Japan in treacherous conditions in Nagoya earlier this month.
Tommy Smith is expected to slot straight back into the squad in place of Durante as he continues his comeback from a hamstring injury.
New Zealand have qualified for the finals just twice before, in 1982 and 2010. They were hammered 9-3 on aggregate by Mexico in a playoff for a place at the 2014 finals in Brazil.
New Zealand Football said on Thursday they had pre-sold more than 30,000 tickets for the home leg at Wellington Regional Stadium, with more than 20,000 snapped up in the first hour of sales on Tuesday.
NZF Chief Executive Andy Martin said the response was a "great result for football in New Zealand".
"There is phenomenal interest in this game and it is only going to grow as we count down to kick off," he added
(Reporting by Greg Stutchbury; Editing by Peter Rutherford)
