Horowhenua Kapiti prop Jordan Tupai- Ui scored a try, as did Wairarapa Bush winger Moo Moo Falaniko, also adding a conversion.
Manawatu, guided by former Whanganui-based coach Shane Ratima, landed a penalty in reply.
The Heartland Hurricanes had to defend with 14 at one stage of the second half after Horowhenua Kapiti reserve Moses Pearce was sinbinned.
Whanganui's Desmond Tyrell was named man of the match for a strong performance from second-five.
Jason Myers covered openside flanker, while Kohlt Covney played the first 45 minutes at hooker, having a hard time with the lineout throws in the slippery mud.
Shaquille Waara, in his second year with the team, came onto the wing for the last 15 minutes.
The Heartland Hurricanes big test for the tournament will be the Wellington Under 19's, who they play this weekend in Palmerston North.