Having suffered a muscular tear in his left side during the ODI Series against Pakistan, batsman Taylor has not reached a point where he'll be fit to partake in the final test.
Left-arm spinner Santner's right foot has also not healed to a level which would allow him to participate, after he sustained bone bruising during the Chappell-Hadlee series.
Coach Mike Hesson said it was unfortunate for the pair to miss out.
"Everyone wants to play against Australia, so both guys are understandably disappointed to be missing out," Hesson said.
"The players and the medical staff worked hard to be available for the match, but in the end ran out of time.
"Ross is back hitting balls again and is targeting a return in the Island of Origin match before we head away to the ICC World Twenty20.
"Mitch is on track to be fit for the ICC World Twenty20 and we'll continue to monitor both players closely."
Mark Craig and Henry Nicholls will remain in the Black Caps squad for the second test.
