Van der Flier was initially named as a replacement and his spot on the bench will be taken by Jordi Murphy for the crunch clash between the top two ranked sides in the world.
Leinster flank Leavy did not train on Thursday, but was named in the side by coach Joe Schmidt.
He also failed to take part in the captain’s run on Friday and has now been withdrawn with his coach suggesting earlier in the week that the 24-year-old was "stiff and sore".
"He's just been sore from the week before. Full-body soreness. Nothing too specific," Schmidt told reporters.
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"As a result he didn't sleep overly well, which is another warning sign for us that if we push him too hard he would fall under that fatigue and not be better."
Schmidt also backed Van der Flier earlier this week, saying he was a stand-out performer when Ireland lost 21-9 to New Zealand in Dublin in 2016.
"I don't know if you remember the last time we played the All Blacks here, Josh van der Flier had a phenomenal entry into the game. He had two searing line-breaks and really impressed," he said.
Ireland are seeking a first win over the All Blacks in Dublin, which would be a major boost heading into next year’s Rugby World Cup in Japan, where they are among those expected to challenge New Zealand for the global crown.
Team: 15-Rob Kearney, 14-Keith Earls, 13-Garry Ringrose, 12-Bundee Aki, 11-Jacob Stockdale, 10-Jonathan Sexton, 9-Kieran Marmion, 8-CJ Stander, 7-Josh van der Flier, 6-Peter O'Mahony, 5-James Ryan, 4-Devin Toner, 3-Tadhg Furlong, 2-Rory Best (captain), 1-Cian Healy
Replacements: 16-Sean Cronin, 17-Jack McGrath, 18-Andrew Porter, 19-Iain Henderson, 20- Jordi Murphy, 21-Luke McGrath, 22-Joey Carbery, 23-Jordan Larmour.
(Reporting by Nick Said; Editing by Toby Davis)
