A blitz of Otago tries in the first 43 minutes appeared to kill the visitors' hopes at Forsyth Barr Stadium.
They led 29 - 16 at the break and struck early in the second spell from a poor Dan Hollinshead chip into a posse of defenders.
The ball ended up in the worst possible hands for Bay of Plenty, those of speedy Matt Faddes.
He raced 95 metres for the try, with Hollinshead chasing hard but only getting a hand on the centre before he powered away to the line.
As replacements flooded on the game turned Bay of Plenty's way and despite being 16 - 43 down, they looked capable of overhauling Otago until the home side managed to close the game down.
It was a good win for Otago, but not without some luck.
Otago found fortune late in the first half, scoring tries from generous video referee decisions.
Fullback Tony Ensor was given the benefit of much doubt in grounding of the ball, after a spectacular leap ahead of three chasing Bay of Plenty defenders. And captain Liam Coltman also got a favourable nod after driving over the line in a mass of bodies.
No. 8 Naulia Dawai scored Otago's first, although he couldn't repeat the effort a few minutes later after working a great move with halfback Josh Renton. Ensor's wonderful catch and pass from a chip ahead set up Faddes' first try.
Otago: 43 (Matt Faddes 2, Naulia Dawai, Tony Ensor, Liam Coltman, Fletcher Smith tries; Peter Breen 4 con, pen, Smith con)
Bay of Plenty: 30 (Culum Retallick 2, Nick Evemy tries, Dan Hollinshead con, 3 pen, Evemy 2 con).
Halftime: 29 - 16
