Counties stormed ahead in the first half with two converted tries from Portia Woodman and Renee Wickliffe also diving over to take her side 19-0 into the break.
Woodman completed her hat-trick early in the second half before it was all Manawatu pressure. Sarah Goss powered over shortly followed by Kristina Sue.
Counties were down to just five players at one stage allowing Sue to touch down for her second try late on, but it was all too little, too late.
Players had the chance to impress Black Ferns Sevens head coach Allan Bunting who will be naming his squad for the 2016-2017 HSBC World Sevens Series after the tournament.
Bay of Plenty's Kelly Brazier was awarded women's player of the tournament and Bay coach Victoria Grant also said Rotorua's Autumn Stephens, Rebecca Kersten and 16-year-old Tynealle Fitzgerald were stand outs for her side.
Grant added that although disappointed her side were knocked out of the Cup quarter-finals - losing 19-0 against Waikato, she was "satisfied" with her team's end result.
"We can really grow from this result and we are very much a future team in the making," she said. "As soon as we lost the quarters we wanted to delete that game. We were well prepared but just didn't front up.
"But we took the positives from it though - we were very hungry to finish the tournament on a high. We showed real quality in our next games and this side is only going to grow and develop - give it a couple of years' time and we will be a major contender.
Grant's focus will now turn to coaching Baywide women's side Rotoiti this season.
Full 2017 Bayleys National Sevens results here:
