The home team led 7-6 at the break.
Impressive left winger Hopoate Finau got on the end of the grubber kick from first-five Finn Hurley to score the game’s only try.
Thereafter the sides traded penalties and Otago Boys’ landed the crucial one three minutes from the end.
The top four sides in the premiership are more evenly matched than they have been in recent years and it has added to the excitement of the tournament.
Southland Boys’ won the opening round fixture between the teams and Otago Boys’ coach Regan Turoa said the game could have gone either way.
"It was a good old-fashioned battle in a bog, pretty much," he said.
"The conditions meant there were quite a lot of errors in the game. But we managed to shift the ball quite well in certain parts of the first half.
"We created a really nice try.
"From there it was an arm-wrestle."
Otago Boys’ had the advantage in the lineout and the scrum was even. But the visitors had the better of the breakdown.
Blindside Jackson Bevin and hooker Jack Taylor shone for Southland Boys’.
But Otago Boys’ No8 Semisi Tupou Taeiloa carried strongly and won the final penalty from another powerful hit-up.
Fellow loosie Jacob Bolwell dominated the lineout and Filipo Whitehouse-Opetaia-Tovio was impressive in the midfield.
Otago Boys' Rugby Club was celebrating its 150th year.
In the other premiership games, King's beat Mt Aspiring 103-3 and John McGlashan beat South Otago 29-7.
In the championship, St Kevin’s edged Dunstan 36-29, Waitaki Boys’ recorded a comfortable 36-10 win against Otago Boys’ 2nds and Wakatipu beat Otago Combined 29-12.
