The 28-year-old Smith, who scored his highest test score of 239 in the third match of the series against England in Perth, also picked up his second test player of the year award.
"I'm pleased that I can be sitting here today and be recognised for what I've done over the year," Smith said.
"I don't play for these kind of awards, I play to try and help the team win and stand up as the leader of the side... It's been a challenging year and I'm proud of the way I have accomplished a few things," he added.
Smith, who also won the Allan Border medal in 2015, accumulated 246 votes ahead last year's winner Warner (162). Spinner Nathan Lyon (156) was third.
All-rounder Ellyse Perry won her second Belinda Clark Award for the best woman player and Warner was named top one-day player for the second year in succession. Aaron Finch took the Twenty20 award.
(Reporting by Shrivathsa Sridhar in Bengaluru, editing by Ed Osmond)
