Otago had its chances to win the game, and clearly scored a try with a minute and a-half left, but it could not break a determined Manawatu outfit which stood tall under the pressure.
Otago led 12-7 at the break, but poor starts in both halves ultimately cost it the game.
The match was all but decided with 15 minutes left when Otago put together more than 20 phases but could not find a way through the Manawatu defence.
Otago went close five minutes later but was stopped just short of the line.
Then from a 5m line-out with two minutes left, Otago drove over and blindside flanker Adam Thomson clearly scored but referee Vinny Munro failed to see the try, and ruled the ball had been held up.
Otago, though, should have scored before then but it picked wrong options at times and was unable to put players into space.
It had a mountain of territory and possession in the last quarter of the game.
Otago's players were content to hit the ball up, offering tackling practice for the Manawatu players.
Otago assistant coach Bruce Carvell paid credit to Manawatu's ability to defend its tryline.
He said some opportunities were lost in the first half, when players were not patient enough, and that kept Manawatu in the game.
"If we could have gone into the break 10 to 12 points ahead, then that might have knocked the sails out of them," he said.
Carvell said he was certain Thomson had scored near the end, but "that was rugby" and the side had to accept the decision.
Manawatu scored two tries in the first 10 minutes of the second half.
Fullback Kurt Baker went over after a good chip from second five-eighth Johnny Leota, and winger Casey Stone crossed after a basic backline move, though poor a defensive read from the Otago backline played a part in the try.
Otago started slowly and had not even touched the ball when it conceded a try, after four minutes.
Classy Manawatu first five-eighth Aaron Cruden made a break, brushing off four tacklers, and linked with his support to send Stone, a former Otago B player, went over.
Cruden added the extras.
Otago put some phases together and winger Karne Hesketh went over after 16 minutes.
The visitors moved the ball to both sides of the field and from a ruck near the line Hesketh got the ball and barged over.
Chris Noakes added the conversion from the sideline to tie the game up.
Otago's first half was littered with with dropped ball and forward passes, but right on half-time it went ahead with a classy try.
Hesketh tore down his wing on a weaving 50m run, beating two defenders, then fed fullback Ben Smith, who ran 20m to score.
Hesketh was the best for Otago, while flanker and captain Alando Soakai got through plenty of work at the breakdown.
Locks Hayden Triggs and Tom Donnelly ruled the line-out.
Manawatu's best was Cruden, while Baker looked good.
Former University A skipper Doug Tietjens played well on the openside flank, and lock Michael Fitzgerald ran hard.
Manawatu 19 (Casey Stone 2, Kurt Baker tries; Aaron Cruden 2 conversions), Otago 12 (Karne Hesketh, Ben Smith tries; Chris Noakes conversion).
Half-time: 12-7 Otago.
