It was left to Tauranga Boys' College newcomer Ben Musgrave, playing just his second game for the Bay's premier team, to keep his team in contention.
When Musgrave went to the wicket the home team was in trouble at 163-6, but a 10th-wicket partnership of 33 between Musgrave and Tony Goodin helped Bay of Plenty to 216 all out in the 93rd over.
Manawatu got to 50-2 by stumps and on day three simply took control of the match to grab the Hawke Cup by way of first innings points.
David Meiring scored a fine 128 runs off 201 balls, with Dane Cleaver, first cousin of Kane Williamson, smashing an unbeaten 102 from just 86 balls.
The match concluded in mid afternoon on Sunday with Manawatu reaching 315-6.
Bay of Plenty bowler Tony Goodin returned 3-69, with his three wickets taking his tally to a remarkable 34 in just seven Hawke Cup games.
Bay coach Ben Williams was in a philosophical mood after the game, realising that all cup runs have to end sooner or later.
"One bad session cost us and we obviously didn't form any partnerships and lost wickets in clumps," Williams said.
"We didn't get any momentum and gave them the ascendancy so it was always going to be hard fighting back with a pretty small total on a good batting track.
"They were good enough to exploit us and cash in. "
Williams noted Bay of Plenty sorely missed last summer's run machines in Joe Carter and Bharat Popli who have been promoted up to the Northern Knights.
"We did have a new-look, inexperienced team but I am still very proud of the way the boys applied themselves and were still competitive even with minimal runs on the board," said Williams.