The music star, 72, was performing at Auckland's Mount Smart Stadium on Sunday when he lost his voice and broke down in tears on stage.
In footage shared by fans on social media, Sir Elton is seen crying as he is escorted from the stage while thousands of concert-goers give him a standing ovation.
"I was diagnosed with walking pneumonia earlier today, but I was determined to give you the best show humanly possible.
"I played and sang my heart out, until my voice could sing no more.
"I'm disappointed, deeply upset and sorry. I gave it all I had.
He shared a picture of himself accompanied on the stage by a member of the crew.
According to one fan on social media, Sir Elton had told the audience earlier in the show: "My voice has completely gone, I'm so sorry."
He was tended to by a medic for around five minutes earlier in the set and continued to play before he was forced to stop completely.
Following his departure from the stage, one fan tweeted: "Sir Elton John - you gave it everything you had - so sad you had to finish your concert in Auckland an hour early after your voice gave out.
"Hope you feel better soon."
Sir Elton is due to perform two more concerts in Auckland on Tuesday and Thursday as part of his last ever tour, Farewell Yellow Brick Road.
According to the American Lung Association, walking pneumonia is a "non-medical term for a mild case of pneumonia".
Generally called atypical pneumonia, it can be caused by bacteria or viruses and symptoms, including a cough, fever, chest pain, mild chills and a headache, are similar to that of a bad cold.
Symptoms are usually mild enough for a sufferer to be able to continue their daily activities.
Sir Elton's Auckland show came less than a week after he won an Oscar along with his long-time writing partner Bernie Taupin for best original song for their Rocketman track (I'm Gonna) Love Me Again.