The visitors had the best of the first half and led 19-10 at the break.
Fullback Liam Edwards made some decisive touches and second five-eighth Mike Collins was elusive in the midfield.
But Southland clawed its way back into the match through its powerful forward pack.
The home side was strong in the set pieces, particularly the lineout, and denominated territory.
Otago Boys' was guilty of some ill discipline which did little to advance its cause.
"It was quite an even tussle," manager Brian Ashwin said.
"Our line-out lost its way a little and they certainly had a bit of pressure on our scrum with their second shove.
"Other than that, it was very even. We certainly had some chances which we didn't take."
The four-point win leaves Southland Boys' well-placed to reach the final.
In the other section 1 match, Gore High School secured a 13-8 win against King's High School.
The teams drew 25-25 when they met in an earlier round-robin match and the game was evenly contested again.
King's scored an early try through first five-eighth Gifford Henry. He also added a penalty.
But King's was reduced to 14 players midway through the opening half and the visitors seized the momentum, mounting a series of attacks and leading 13-8 at the break.
Both sides had chances to score in the second half but had promising attacks snuffed out with scrambling defence.
In section 2, Verdon College scored a late try to beat Waitaki Boys' High School 12-8 in Oamaru, and John McGlashan College scored five tries in a 29-7 win against Dunstan High School.
In section 3, St Kevin's College thrashed South Otago High School 40-12 in Oamaru, and Kavanagh College scored seven tries in a 41-12 romp against Central Southland College in Dunedin.
Centre Guy Woodhouse snaffled four tries.
