"I was diagnosed with walking pneumonia earlier today [Sunday], but I was determined to give you the best show humanly possible," he said in an Instagram post after the concert. "I played and sang my heart out until my voice could sing no more."
Walking pneumonia is an infection caused by bacteria that mostly affects people's respiratory tracts. It's less severe than other forms of pneumonia but can still leave people feeling sick.
Despite efforts to battle through his set, he was forced to cut the show short.
Sir Elton was given medical attention on stage while paramedics were seen waiting with a stretcher in case he collapsed.
"I'm disappointed, deeply upset and sorry. I gave it all I had," he wrote on Instagram.
Sir Elton's premature departure left multiple fans in tears.
"He tried so so hard... but his voice was completely f**ked," one told Newshub on Sunday.
"Just feel so sorry for him."
Sir Elton is performing six shows here on his Farewell Yellow Brick Road tour which covers five continents across 300 shows.
At this stage, it's unclear whether his next Auckland shows - on Tuesday and Thursday - will go ahead.
He first visited New Zealand in 1971 - playing Auckland's Western Springs Stadium. Since then, he's brought at least 12 more tours to Kiwi audiences.