The pressure compounded for the home side when halfback Te Ra Whata was shown a yellow card two minutes later.
It meant Rotorua, who were leading 29-27 at the time, had to hold on for the last three or four minutes with only 13 men.
They did more than that though, pinning Scots College (Wellington) deep in their own half before Rotorua's Kaydis Hona sneaked a try to seal the match.
Boys' High fans ran on to the field to celebrate with the champions after the final try, but they were quickly removed from the pitch so Kaleb Trask could attempt the conversion.
Trask added the extras to make it 35-27 and the fans ran on to the field a second time as the final whistle blew.
"It is something that has not come easy. It is a pretty special moment and we can finally say we are the best in the country," Rotorua Boys' coach Ngarimu Simpkins said.
He said they could have chucked it in during the match, especially late on, but his side showed a lot of character and determination.
"We believe in our character and our school system of developing strong men and I think that is what got us through in the end."
It is the fourth time the school's 1st XV have been crowned national champions, with the last title coming back in 2003.
The final yesterday was played in stark contrast to Rotorua's semifinal two days earlier, which saw the home team grind out a 7-5 victory over Auckland's St Kentigern College.
There was some brilliant running rugby on display from both sides, which produced some stunning tries.
Rotorua captain and fullback Isaac Te Aute had perhaps his best game in a Boys' High jersey, scoring two stunning individual tries, the first of which saw him go 50 metres and beat about four defenders.
Trask, Ngarohi McGarvey-Black and James Tofa were also in top form, causing plenty of trouble for Scots' defence.
The victory yesterday will likely see Rotorua Boys' attend the 2016 Sanix World Rugby Youth Invitational Tournament in Japan, pitting the best schoolboy rugby teams from across the world against each other.
-Rotorua Boys' High School 36 (James Tofa 2, Issac Te Aute 2, Te Ra Whata, Kaydis Hona tries; Kaleb Trask 3 con) beat Scots College 27 (Alex Fidow 2, Jack Gray, Peter Umaga-Jensen tries; Malo Manuao pen, 2 con) HT: 19-12.