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"I'm sorry, so very sorry," a distraught John told the Auckland crowd on Sunday night.
He broke down in tears and needed to be assisted from the stage after attempting to launch into Daniel, but having no voice left.
The song was number 16 in a 25-strong playlist at Mt Smart Stadium.
John's next two Auckland concerts, on Tuesday and Thursday, are now in doubt.
Earlier he had struggled to perform Candle in the Wind and told the audience he did not know how long he could continue as he "had nothing left". He left the stage just after 9pm and the stage, screens and stadium were left in darkness.
However he managed to return to the stage about eight minutes later in a new costume.
The concert was also paused for almost five minutes straight after John completed Someone Saved My Life Tonight about 8.40pm.
John remained on his piano stool as assistants - and what appeared to be medical staff - tended to him. Some concertgoers believed his blood pressure was being taken as the assistants spoke to him.
There were no announcements and John remained on stage. After several minutes and without speaking, John continued the concert with the song Levon.
The large screens flanking the stage had briefly gone dark but within minutes the concert resumed - to wild cheers from the crowd at Mt Smart Stadium.
John had told the crowd he was determined to carry on with his first Auckland show.
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John has resumed his tour of New Zealand after jetting back from Los Angeles to attend the Academy Awards.
The Auckland leg of the superstar's New Zealand tour comes in the middle of the longest dry spell on record.