Trailing 14-18 with three minutes left, the Maori engineered a superb try down the right side with a Tamati Ellison break finished off by big loose forward Thomas Waldrom.
Piri Weepu converted from wide out.
But there was still some anxious moments when Australia A were awarded a penalty after the hooter had sounded. But Wallabies utility Mark Gerrard came up just short with his 45m attempt and New Zealand Maori claimed another famous win.
Two points behind the Austraians in the championship going into this final round, the Maori had to win the match to take the title and keep New Zealand's proud record in the tournament going after the Junior All Blacks had won the previous titles.
Had the match finished in a draw, Australia A would have won the title because they had banked 19 points from their previous four matches to the 17 of New Zealand Maori and had a far superior points differential.
Two tries from league convert Timana Tahu appeared to have placed Australia A on track to condemn New Zealand Maori to defeat.
However, co-captain Tamati Ellison atoned for some earlier defensive lapses on Tahu to set up the matchwinning score when he darted down the right flank before inpassing to Waldrom to surge over.
New Zealand Maori led 14-7 at halftime thanks to tries to Tanerau Latimer and Liam Messam before Australia A regained the ascendancy until the dying stages.
Australia A 18: Timana Tahu 2 tries; Mark Gerrard 2 pen, Daniel Halangahu con.
New Zealand Maori 21: Tanerau Latimer, Liam Messam, Thomas Waldrom tries; Piri Weepu 2 con, Callum Bruce con.