Otago led 8-0 at the break but the two sides were locked 13-13 at fulltime. Manawatu missed a late penalty in golden point extra time that would have sealed the win.
But with the scores still level, Otago claimed the higher finishing spot courtesy of having scored the first try.
Coach Luke Herden said miserable conditions turned the game into a ''chess match'', with both sides keen to play the game in each other's half.
''For the resources we had available, I think the boys punched above their weight and should take a lot of confidence out of it,'' Herden said.
''I look forward to seeing some of their names in the premier [club] competition next year and the Mitre 10 Cup over the next couple of years. There are a few of them who have potential.''
Front-rowers Teague McIlroy and Kilipati Lea, midfielder Thomas Umaga-Jensen and outside backs Taylor Haugh and Josh Buchan had strong campaigns, flanker Slade McDowall was ''outstanding every game'' and fellow loosie Ben Scorgie was tireless.
